I get that pain always seems to be pluralized in Danish, but I feel like the translation should be singular. "I have pains in my leg" sounds kind of unnatural to me.
From a logical point of view "pains in my legs" is also correct, as your leg can hurt in multiple spots. In my opinion, "pain in my legs" conveniently avoids all those little differences and still conveys the same message while sounding better.
Yes, "a pain in your legs" rolls off the tongue better, but in my previous occupation I have heard quite a few of my colleagues complain of "pains in their legs", even when they had no legs.
No, because: "Benene" = "The legs"; and you can't say ".....his the legs." Ben=leg, ben=legs, benet=the leg, benene=the legs.
Not much difference really.
"Jeg har smerter i benene" = "I have pains in my legs".
"Jeg har ondt i benene" = "My legs hurt".