We know that Ganondorf must have been reincarnated at least once, before
FSA.
We also know that Ganondorf has been killed at the end of WW and
TP. There are also theories that the "spirit" of Ganon is seperate from Ganondorf, (perhaps Ganon is only dormant inside of him?) and has appeared in his monster form multiple times.
Putting this all together, we do indeed come up with inexplicable returns of Ganon, at the very least, whereas Ganondorf's one return is explained. (He does have one more inexplicable return if you don't place
ALttP after
FSA). What we have so far supports the idea that Ganon can come back to life very easilly, (most likely through unknown ressurection rituals, as he needed one in OoX).
Honestly, though, I take the Zelda series to be full of symbolism more than anything, especially in it's characters. Ganon is just a symbol for the bad guy, the ultimate evil that many Links had to face. Until there is some sort of continuity in Ganon's returns, I don't think the matter can be explained fully. Unless you beleive his spirit is just straight up immortal, and "killing" him only banishes him temporarily.