Yes, the number of bases do make a difference within the rules, unless you make allowances.
3 stand cavalry would start with an extra d6 over 2 stand cavalry and foot in melee/close combat. Also, your maneuver column depth, in the rare instances you use that formation, would be way off.
Dragoons are 2 stands as cavalry, but 1 stand when dismounted; your larger dragoon units will need to be accounted for in the shooting phase.
Of course, as Barry has written before, you've bought the rules, now play them as you see fit and as you can get your opponents to agree to.
For me, I would elect to treat 3 stand cavalry as 6 figure units on 2 stands, with the extra stand just for show.
What really matters though, is how many figures the unit is comprised of on the roster, not how many are physically based with the unit.
There are a few other nuances with having an extra stand, but it really is up to you as to how to play the game with your mates.