From what I've read
1)they lowered the limit from 99 to ~30
2)they don't expire, you just stop getting new ones.
Personally I think it's a little silly to hold on to encounters. I know some are good for completing excellent throw research, but since there is no real way of seeing what the encounter is any more than a couple is a waste. And as far as using them for lucky eggs, that's super inefficient vs. mass evolving