Gibbo,
I have installed canopies both new and replacement. All have been drilled and pop riveted or machine screw. I have never experienced a crack while installing. There are some simple precautions that will help with avoiding cracks.
Keep the plastic warm, about 80 deg.F works well. Warmer is not better, the material expands and contracts quite a bit in the normal temperature range. Fastening while too warm will cause stress after cooling.
I have used both plexiglass drill bits and dulled HSS bits. Either one works. Dull a HSS bit by running it in concrete for a few seconds. While drilling don't push very hard and have a hardwood block supporting to prevent pushing through.
If drilling over the steel canopy frame keep the bit aligned to the contact point of the tube and plastic. This will prevent glancing as the bit comes in contact with the frame. Use a bit that is slightly larger than the fastener, pop rivets expand while pulled and will cause pressure in the hole. Drill the frame with the correct size bit for the fastener.
An easy way to find the contact point of the frame to the plexiglass is lightly wet with water or window cleaner. Hand squeezing the two together will reveal a line at the contact point.
As I was typing, I recall mistakenly using steel mandrel pop rivets on one install. That aircraft has been flying for years with no cracks.
Take your time.
Also, I am not against SikaFlex. It looks like a good system, just never had the opportunity to use it.
Cheers!