Question about encoding video

I just set up my first Plex server and found that I have to convert all of my totally legally obtained MKVs to MP4s to run on Plex.

Right now I'm encoding them with HandBrake and it's taking ~30 mins per file and using 100% of my CPUs capacity (running around 80 degrees C).

Is this how most of you guys do it? or am I missing something? I'm concerned about hurting the lifespan of my CPU. Would using my GPU to encode be a better option?