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They will recrawl it but equally important is that traffic following links to your site will get where they're supposed to go. A good rule of thumb with search engines as well as humans ... it's never too late to do the right thing. 
(Of course, with a Penguin penalty you might go bankrupt before they get around to rewarding you for good behavior) 
Hope that helps !
What you're referring to was discussed by John Mueller a while back and Andy's right ... it's devalued.
You can read a bit about what John said or listen to it yourself at https://www.seroundtable.com/google-hidden-content-tabs-19534.html.
Cheers.
Will respond via PM ... just noticed multiple listings which is a direct violation.
Sorry about that code. Ordinarily I'd have had a chance to test it but didn't have a test site ready for that type of testing.
Thinking about it further, an actual redirect won't work due challenge/response on the certificate not being installed. If you load the site in a new browser you'll see what I'm talking about.
If the site were mine (or a clients of course) I'd recommend getting a certificate setup and redirecting the whole thing to HTTPS now. If you don't want to do that the certificate will at least light up the HTTPS site directly (i.e. without the insecure warning) which will allow it to be redirected properly.
That said ... you do have the canonical tags on the pages properly so a duplicate content warning will be a false positive in that the content is indeed duplicated but Google knows that the HTTPS is the primary source as far as I can tell. Your site is going into a redirect loop on HTTPS so I can't double check but it appears as though it should from the way it's displaying in the source. Happy to double check after the loop is corrected.
Dave
Eric Ward did a good Hangout last Friday and gave them the nod too. the full 1hr 48min is at but but the short answer matches the answers above. If it makes sense for your user, it makes sense for Google. I think I hear Matt say that once or twice too.
When I visit https://www.kimwist.com/ it's spinning into a loop and doesn't display the site. You can check it at http://www.redirect-checker.org/ and see what I'm talking about. It looks like it's 301ing to itself. I'm wondering if you've set a redirection to go to https that's trying to do it if the URL itself is https in which case you'd want to switch it to point to http.
Are you referring to the toolbar PageRank (the green bar)? If so, it hasn't been updated in ages and most likely never will be again.
That said, this was only a visual representation of what Google saw. PageRank as a Google metric is still performed internally and as far as I know, in realtime so PageRank passes - you just don't see it.
If you're referring to "page rank" meaning the actual rankings of a page - for that we'd need to see the pages themselves to know why they're not ranking is the category pages are doing OK.
A 200 is perfect (it just means "OK"). I double-checked and your canonicals' are pointing to the http version which is also what you want if you're not doing a 301. Some tools will still show a duplication even with the canonicals but rest assured ... Google knows what's what.
Best of luck to you as you proceed forward and glad it worked out.
Regards.
Dave
Question one might be - why is Google deciding that's the most important information on the page? If you have a well-worded description tag and quality content, what is missing from what you're doing that this donations area is what they're grabbing onto?
Generally I've found that if the wrong information is being displayed as a description int he SERPs, it's generally a shortcoming in the description tag or content.
Assuming that's all working, heck you could use something as simple as an iframe to "hide" the content. Technically Google can crawl iframe data but I'd bet dollars to doughnuts (whatever that means) that if you did this it certainly wouldn't show up in your description tag. The perk to this being, it is kinda-crawlable so it's not "hidden".
It seems to me that this is more just decent SEO getting rewarded over time. Knowing when your site jumped up would help though.
Back in 2007 Matt Cutts announced at Pubcon that sub-domains and folders were to be treated the same. Of course, that didn't exactly happen as it was supposed to but the principle is sound. If what you're worried about is how weight is passing then it's pretty much a level field where you're left to chose the one that makes the most sense for your backend. I personally tend to lean on sub-directories whenever possible for predictability and simplicity.
I will note that I have quite recently seen penalties against a sub-domain on a large-scale site affect the rankings on the domain as a whole so there's definitely crossover in domain authority and trust.
The quickest answer to your question is, yes the domain will benefit from the sub-domain. But it's probably still easier to use a folder.
One can never write off an algo change of course (especially given that there were 3 Panda updates from late August though September) but if so it was probably a case of you having good content (congrats) and solid links from domains that held their value through the updates and being rewarded during this period via the decline of others.
Or one could simply say, "We have good content and links from good sites so our rankings improved."
I have to agree with Oleg in going one-to-one redirects of any pages with links or incoming traffic. Most hosting plans will let you have multiple domains so setup the one you're "not using" and just one-to-one them in the htaccess file. Remember - it doesn't need to be every page on the site, just the pages with links or entry traffic.
Speaking on links, when you're choosing the domain to use as the primary I'd be sure to very strongly consider which one has the best link profile. A bit is lost in a 301 so better not to lose that.
Via Search Console try to "Fetch As Google" and assuming that works without errors use the submit function. You'll know very quickly whether you've got technical issues and get the page into the index very quickly.
Which manual action notice did you get? I'm assuming from what you noted that it's the user-generated spam notice but thought it better to check before replying. The only other one I can guess might apply was the unnatural links penalty. If it was the unnatural link penalty then you'll have to wait for the next Penguin update but if you can confirm the penalty I'm happy to look into it further.
Regards.
Dave
Hi galwaygirl.
I'm going to be PMing you my thoughts as I've taken a bit of a peek at your backlink profile and my advice is specific only to your scenario and might be taken wrong and applied to others incorrectly if anyone else read it.
Dave
Provided that there are no links to http://clientname.com/products/ and obviously it's not part of the breadcrumbs you're fine though you may want to consider adding these pages to give you a point to all products (of a list of categories of products), etc.
But no ... the structure itself isn't inherently going to cause problems.