Hi BBuck,
I think I understand what you're saying, and there are 2 separate issues that I see you've brought up
First, while there's nothing necessarily wrong with distributing navigation the way you've described, I find from a UX (user experience) standpoint that this is best avoided. Aside from that, I'm unaware of any reason it would be a bad practice.
As for the URL issue you mention in the second paragraph, that can be taken care of with 301 redirects / rewrites. Basically, take this example: I have a page that's www.example.com/familiar/general/specific, but I don't want such a long URL. Using 301 redirects and rewrites, I would have the page stay the same, but the end of the URL could be whatever I want, like www.example.com/specific. If you're unfamiliar with how that works, I suggest either hiring a developer to do it (which would take a few seconds per page), or finding a quick tutorial if you have access to your website's back-end.
I hope that helps you!