The reason why hammer pickup isnt automatic is that some hammers do more damage than others.
Well that really isn't a good reason. It's a completely hidden (and non-impactful) feature. Everything dies in one hit no matter the hammer and the player can't see the damage values in any way to better choose some hammer over another.
I suppose so, but your point about everything dying in one hit is not exactly true. Some rooms have enemies with more health.