I know that some have had problems with WD-40 penetrating primers and .22 ammo, but suspect the problem may have had more to do with poorly made ammo than with WD-40 itself. (In other words, the same rounds immersed in water may have performed in a similar manner.)
I've actually TRIED to disable some rounds with WD-40, immersing the ammo in enough WD-40 to cover the round in a small aluminum cup -- and left it there for a week or two. In that case, which was some old 9mm rounds and some .22, it had no effect. (That's not to say it won't affect other rounds.) I should have tried penetrating oil, too, but didn't think of that possibility until I was typing this response.
I suspect WD-40 CAN be harmful to ammo -- but it may have more to do with ammo quality control (and a round's inability to keep moisture out) than with WD-40, itself.
I suspect, but have no proof, that a passing, modest exposure to WD-40 will have little or no effect on most ammo. But I'll just keep WD-40 away from my guns and ammo, unless I have a compelling reason to do otherwise.