I've not heard of any sort of limp mode, but it would make sense for Honda to have included some sort of feature that limits engine output in certain fault situations. But I think such systems would normally be triggered by engine or transmission faults rather than tyres?
Actually, if you've fitted a spacesaver spare (rather than a full size spare) then you don't want to go much above 40mph anyway.
Possibly a silly thought, but are you certain that you haven't accidentally set one of the speed limiters at 40mph?
Finally, if you hit a kerb hard enough to blow out a tyre, then you may have damaged something else in the suspension or steering, so should get those checked.