If you've got the nut flush and a straight draw on the flop you've got a 51% favour over top pair/two pair. Personally I would call their shove or go all in because you have to consider the following options in a cash game:
You have AK you have a straight and nut flush?
Could they be bluffing
Are they drawing too? And if you have AK you beat their flush draw (unless it's a straight flush obviously)
If you hit which the majority of the time time you probably will you will get paid nicely.
If you don't hit well just rebuy in.
are good enough for you to call?
And how I play it I would check call a draw, or if I know my opponent is abit of a weak player I would check, re raise, then on the turn about 62 percent of pot. Reason for this is if you have position he will check the turn and then you can fire again and if he's bluffing he will almost certainly fold because he knows you have something via the re raise on the flop.
If he calls you on the turn you know your beat (that's if you haven't hit your flush or straight) so if he calls its on your decision to bluff the river if you missed or check fold the river. Profitable in the long Term.
Hope this helped