Does time machine work with the trash folder?

Things should only be put in the trash folder if you want to permanently delete them.

Makes perfect sense. You're equating second chance with stashing stuff you might want to delete later.

The trash folder both Apertures and the systems is not a temporary holding area it's a place to put things that you want to delete. And if you use it as a temporary holding area you will at some point in time get burned.

But to answer your first question TM does incremental backups. So if go delete something from your system eventually if will also be removed from TM. how long before it is removed depends on the size of your backup drive and the amount of changes you have to your file system.

So make a top-level Project called "_Circular File". Put Images in there that you what to have out of your way but not discarded.

It really is good and proper to treat the Trash as trash. I instruct everyone to _empty_ the Aperture Trash at the end of _every_ session. The reason is this: it is the only time you will remember whether it is safe to delete the items in there. If you wait, you will then waste time trying to answer "Did I really mean to throw that out?" or, periodically, you'll give up trying to remember, and will empty the Trash without reviewing it. At the end of every session, examine the Trash, confirm that the items there are trash, and empty it.

Shocking, perhaps, but you should also empty your system trash every day. The real-life equivalents are good guides here. No-one in an office hoards their trash. If you mean to throw something out, throw it out. If you don't mean to throw it out, do not put it in the trash.

I don't know how TM handles the Aperture Trash. I do know, however, that I would not expect this behavior to remain consistent, and would absolutely recommend against a workflow based on it.