I can understand the expired chart notices--because, after all, AP isn't in business to let us navigate for free. On the other hand--and as you suggested--it would be more pleasant if the notices didn't appear in flight. BEFORE flight, while planning a flight, would be much better, and it would probably work at least as well for AP's cashflow.
I really like your idea about delaying WinCE error messages, especially when one pops up on short final, as it did yesterday. Not sure it's possible, though, because it's an operating system error, not iFly's.
What annoys me most is when I'm on an auto-pay subscription and iFly keeps putting up notices that my subscription is going to expire in [n] days. THAT is annoying.