The extent of the work they did was:
"empty out water, clean and dry internal parts, replace seals & re-assemble, run in tank for 20 min with no issues".
I spoke with the owner of the shop - this is the same place I bought the boat and motor from, and expressed that my concerns are very legitimate for the fact that water damages electrical parts. She told me that if I have another problem even after it's outside of warranty, that there would be a record of the service they performed and when, and that any issues that stemmed from water damage could still be repaired under warranty at that time. Being less than a year old I still wanted a replacement motor or lower unit, so she made a phone call to Minn Kota. The wait time on the phone for her was longer than the amount of time I had on my lunch break from work. I did hear her call another phone number and leave a message stating the situation. I'm still hoping Minn Kota comes through with a new motor for me, cause I just cannot trust that an electrical motor that has been under water will give me years of lasting performance.