1) If you are thru-hiking the AT, the chances are that a few other thrus will taunt you for any choice you make. These few will be dogmatic and insecure people. Pay them no nevermind, unless they try to give you a wedgie.

Because one of your patches identifies with the wobblies, there is a very small chance that a dittohead may remark acidly on your choice of affiliation, but I don't think many dittoheads backpack - or have even heard of the wobblies, so you should be relatively safe on that account, too.

2) If I were going to sew on a patch, I'd consider waxing the thread, just to minimize the chance that the thread would wick moisture into the pack. Needle holes are very small, so any compromise to the pack's integrity should be negligible.

Just HYOH and have fun.