So I've rebooted and even with 2 instances of transmission running and an SNES emulator running, the temperature and CPU seem nominal. The transmission web interface is responsive, sometimes it does get a connection timeout. Not now, though, everything seems to be running smoothly.
I exited back to EmulationStation and tried to browse through ROMs (I have around 300 SNES roms and most of them have been scraped) and the loading of the ROM metadata is a bit slow again, possibly due to transmission writing to the USB a lot. Also, the temperature steadily climbs up to 75 deg C.
Stopping the torrents in the web gui helped with ROM browsing, but the CPU temp still lingered at around 75 even after a minute. I killed the process and temp went back down to 65 deg. C.