Seems I've learned this the hard way today, and after a quick search I found this:
https://bugs.maemo.org/show_bug.cgi?id=10435
Although it says "fixed", so I'm confused...

Namely, I checked my email on N900 today (with its default mail client), and after I got home I didn't get those same messages on my computer. I use POP3 on N900, and "leave messages on server" is checked on all accounts.
It used to work fine a few days or weeks ago, but back then I deleted messages from N900's Inbox only after retrieving them on the computer (whereas today I deleted them right away - so it sounds like POP3 acting IMAPish in this regard ).

So I suppose I should be more careful with this?