Stoppies and fork compression?
 

A few weeks ago I upgraded my front end to use racetech emulators. 0.90 springs and 20W oil. I also put a cable tie around a fork to check how much travel is being used.

With normal riding to work I cable tie is moved halfway up the fork. The other day I found a quiet road to try a couple of stoppies and after that the cable tie is right at the very top. Should the forks bottom out when doing a stoppie, or should there still be a little bit of travel left? Can this cause any damage or am I being a bit paranoid? Would thicker oil help this?

Sounds about right. Thicker oil won't help. It won't make the forks more difficult to compress just slower. It is the springs which determine how hard or soft the suspension is. You should expect to get full travel doing stoppies. 1/2 to 3/4 travel on normal riding is about right.