Yes,..
It does take away some support for the carb, and will put more stress on the intake connector... (I haven't heard of one breaking from it)...
They are more exposed, and so, will get dirty faster,.. also wet...
They'll make more intake noise...
More air turbulence going in the intake...
You'll have to get another filter for your crankcase breather... which may blow some oil around yer' engine...
They usually have less filtering area,.. so they do less filtering...
A K/N in the stock airbox will do better and give better performance,.. but If you like the look, get a cone...
Cones are cheaper...
Now, I'm going to be attacked by the cone people...

...
... sounds like a sci-fi movie..."Attack of the Cone People!"...

...