As a DM, I don't let players 'suffer' for making a decision to use a weapon (or other option) that is less efficient, but character appropriate. If a rogue uses a dagger because it fits his character better than a rapier, I'll make sure that the difference between the dagger and rapier (in terms of damage) is closed or overcome.
For example, I might let them find a magic ring that does not require attunement that allows them to roll a d8 for damage with any piercing weapon, or they might find a poisonous sheath that allows them to deal an additional d6 poison whenever they hit on an attack made before the end of their next turn after drawing a dagger from the sheath.