It depends on what you do with the switches, after clipping them.

Clipping 5-pin switches down to 3-pin doesn't create any problems, unless you want to later use those switches in a plateless build.
If you're doing a plateless build, the extra two pins will help keep the switches aligned properly, which is normally handled by the plate, when using 3-pin switches.
I've seen some really horrible looking plateless builds, where the keys are all just aligned haphazardly to each other.