Virtual Hub Page Impact

[APFM]

I currently have a website structure that has multiple subfolders.

One of the primary sub-folders has hundreds of pages within (e.g. www.mydomain.com/subfolder1/page)

The pages are all accessible through other subfolders, as contextually appropriate, but there is no existing hub page for the specific pages. In other words, while www.mydomain.com/subfolder1/page1....n are all valid URLs, www.mydomain.com/subfolder1/ is a 404.

My question is given that the pages within the subfolder are accessible through multiple other subfolders, how much of an issue is it that the specific subfolder these pages are within 404s.

Does this negatively impact in any way?

[Mobilio]

TL;DR - Yes and no.

There are two cases and i will be descriptive as possible.

1st case is if subfolder are linked from other pages. Like /subfolder2/page2 -> /subfolder1/ or /subfolder1/page1 -> /subfolder2/. In this case you link direct to 404 page and this can frustrate users and bots too. There is also some confirmation that nonuseful 404 page is low quality signal too: http://themoralconcept.net/pandalist.html (#10 in low quality signals). That's why you need to use crawlers and fix 404s - good for users and good for bots too.

2nd case is when users are curios. I'm one of them. Sometime. So let's say we have curious URLs:
http://www.moz-team.com/randfishkin/article1http://www.moz-team.com/randfishkin/article2
http://www.moz-team.com/randfishkin/article3
http://www.moz-team.com/cyrussheppard/article1
http://www.moz-team.com/cyrussheppard/article2
http://www.moz-team.com/cyrussheppard/article3
as you can see urls are very clean and very descriptive. And now add curious user (pick me!) that can want to see more about Rand or Cyrus. This can be page with CVs, short bio or list of all their articles. So just editing URLs to: http://www.moz-team.com/randfishkin/ or http://www.moz-team.com/cyrussheppard/ using backspace. In perfect world this will give information... but in your case 404. And this is not good for users.

That's why it's much better if you can create "category" page for each subfolder even if this isn't linked from other pages. This was explained many times as "silo structure":
https://moz.com/blog/site-architecture-for-seo
http://www.bruceclay.com/eu/seo/silo.htm
http://www.stateofdigital.com/optimising-urls-seo-ux/

I hope that this answer will help. You MUST optimize site for users and bots too.