Depending on the ages of the flower girls you should invite them, if they are toddlers and or younger you may consider talking to their parents to let them know that it is not necessary for them to be there.
This depends on the age of the flower girls and time of the rehearsal. If it is past their bedtime, keep them home. If it is late on a school night, keep them home. If it is an afternoon, let them come.
Absolutely yes, and their parents, also. They are no less a part of your bridal party than the other attendants. Why would you consider excluding them?
Yes. It's important to include all involved with the wedding in all the important events, unless your "grown up" event will include themes or activities not appropriate for them.