Extra holes drilled in a motor mount will weaken the mount some. Depending on the location, it may or may not be significant. If the mount is metal, the strength should still be satisfactory. If it is plastic, I would consider the following. If you have room to move the engine backward (toward the firewall) and drill four new holes, the effect should be minimum. If you have to move the engine forward to drill the new holes I would consider replacing the mount.

Regarding your other question, it won’t hurt anything to drill the motor mount holes to a size to match the ones in the engine, but since it has been flying with the smaller bolts for several years there probably isn’t any problem keeping things like they are. The only advantage I see in re-drilling the holes in the mount and using larger diameter bolts is that there is less chance of accidentally introducing some side thrust by mounting the engine a little crooked.