Deffinatly leave a full saddle patch... saddle rubs cause problems, days that you can't ride, a sweaty saddle patch is easily more preferable than a sore horse.
Rain
Saddle patches are from the age where nunmahs were not used.
Unless you are planning to ride without a numah take it off - after all who likes a washing machine full of hair????
I ahve 5 hunt horses here and for first winter clip the lot comes off, saddle patch and legs! Otherwise come the end of the season you have very hairy legs and back!