I think having the gems as a semi-critical component would be the way to go. That would give people more motivation to collect them due to the mystery of unlocking secret rooms etc, whilst at the same time this doesn't force them to collect them. This would obviously have to be explained to the player at the start, so they know the reason for collecting them and what benefit it has.
I have a fairly low ceiling room, if I extend my arm upwards straight then I will hit the ceiling. I haven't tried this version yet so I don't know how vertical the arm would need to go, but it's just something that makes me wary when seeing reaching up to collect gems.