I'm starting to have this problem now, kinda strange though just left for a bit of exploring and had changed some modules around in the ship, was running a bit hotter so deactivated some mods.
Heat while scooping isn't really a problem unless I have gone several jumps without being able to fuel scoop. deactivating the shields actually kept the ship quite a bit cooler at 63 where with them up i would hit 68 or 69 while scooping and jump to +70 easily when scooping for more then one jump.
Funny thing is I made about 6 or 7 jumps with the shields staying deactivated and then suddenly this started to happen, nothing I have tried so far has reverted this behavior, guess ill just leave them on since its normally not an issue, and I also will submit a report on it.