100% transparent polygons - collisions?

Well, in my project I'm using cylinders that are 100% transparent (alpha).
I'm also using polygon collisions...
Could it be a possible speed issue?
Polygons are not rendered on a screen, but computer still has to check collisions.
Or is it perfectly fine?

You'll get more speed, if your not rendering them, and only using them for collision purposes.

I often use 100% alpha transparent meshes for collision purposes. You probably should try to use simple shapes and low numbers of facettes / sides etc. If collision is not required, you may hide the mesh instead.