I am inclined to lead toward some type of siloing with a high content site. There is the very purest silo architecture which I feel Bruce Clay presents very clearly in his site articles. You can certainly vary it to be less rigid and still be an effective SEO tool.
I generally agree that MOST content should not be too many clicks from the home page, but drop down menus can go a long way to keep a lot of content close without it being unwieldy. Perhaps it will help to look at it this way: the way your structure your navigation tells Google what you believe your most important pages are - if you tell them ALL your pages are equally important, you dilute the ability of your top pages to rank better than your lesser pages.
If that makes sense to you, I hope it helps.
301 redirects are the very best way to redirect and retain the most link power. Within the site, you have nothing to worry about if your new structure has better SEO. 301 redirects do not always pass 100% of external bank link juice, but it's still the best tool we have to keep what we have already achieved.