Unfortunately, as Ganon, the best thing we can do is just take it and try to anticipate their next move after the juggle. Mario is probably the best juggler against Ganon (talented Marios can very easily get 70% off of a low% string), and the same applies to him.
(Note: Sheik's juggles are more dangerous, but aren't as damaging)
Knowing this though, know that these characters will fish hard for these setups at low percents, so act accordingly. That is, at low percents, it's better to get grabbed for 10% than juggled for 50%, so while at low percents, hold your shield rather than spotdodge/roll. Also, if you're at 10% or lower, try to DI (press the stick downward) downward against a Sheik FTilt, Fox UTilt or Mario UTilt. If they're off by a little bit, you'll be able to land and perfect shield.
So yes, frustrating as it may be, such is yoke borne by we Ganons. Just don't panic when you get juggled. Players can usually smell that impatience and neurosis, and just wait for you to make a hasty move. So keep your poise and just roll with the punches. Ganon can match that 50% easily.