On my '91, the lower brackets are enough to hold the windshield fairly steady (not too sturdy though). I haven't noticed much extra vibration from the windshield. My stock support bars are permanetly removed since I built a cage.
Your insurance agent or local law enforcement folks are probably the most qualified to answer your "have no issues" question if that's the type of advice you're looking for from a safety/legal standpoint.
This is what things looked like as I was first disassembling the cage. I have a bunch more, but you probably will see the results with these pics.
Older CJ's didn't have these bars and are law compliant, but I'm not too sure about YJ's unless a cage is added.