I surprised that nobody brought up having a hand crossbow over a normal one or a normal bow. There are some cool combinations with feats that makes that work better, but I never tried, so not sure which ones. Daggers are fine- better when they are magic with the returning property so you only need to carry one. I find a lot of people do not like the d4 damage when you can get a finesse weapon for 1d8 with the rapier. There are plenty of threads for those discussions that you may find worth reading.
I never penalized players beyond the normal making a stealth check, nor heard other DMs doing this. There is the armor penalty talked about above, but to add more is getting to the jerk DM phase. Some players and DMs like more nitty-gritty and use more things like this. I can play by tracking rations and arrows and maybe carrying capacity if needed, but I do not like that style.