Even vanilla items can be made redundant by add-ons. For example I see you've included fire grenades : I've played with them recently, and I find the grenade form so handy that I find very little reason to use the 3 incendiary ammo of the vanilla weapons. In turns, this reduces the interest of those versatile weapons.
I dont think incendiary grenades make incendiary ammo's redundant... I think they were redundant to begin with. Inc ammo isn't very practical for doing damage on anything past sectoids and floaters. So a gun loaded with INC's is much less practical than a gun loaded with something else. INC grenades provide a handy dose of cleansing flame in a convenient package, without having to swap ammo or weapons.
The versatile weapons still have AP and HE ammo so I'd say they're still pretty versatile without the 3rd ammo type. But you could maybe offset the loss by adding in a stronger AP that can be researched? or pseudo plasma rounds? to keep multi-ammo weapons more relavent in the later game.
this is all just oppinion though.