Piercing had its uses but, except for UFO, it wasn't "I pick Marisa because of it" useful.
In EoSD, you pick MarisaB because of Master Spark.
While it has uses in PCB and MoF, Marisa has much better options than lasers.
Piercing is what makes MAlice cannon a thing, so...
SA ReimuB would be a better piercing shot if she didn't also try to be a homing shot
Now, about the games in which she doesn't have it:
In TD you don't really see the need for piercing because most enemies are clumped together, which makes missiles very good for crowd control.
On DDC, MarisaB has both her missiles and a bomb that allows you to attack two places at once (or at least lets you ignore one side of the screen for a while), and MarisaA's flamethrower has more consistent (albeit narrow) range.
Then you have LoLK... Reimu and Sanae have homing, and Reisen's unfocused shot covers half the screen, what does Marisa have? four 3px wide lasers that get stopped by a single enemy, and that in some cases are not even strong to kill it fast.
Lasers are just not good, I don't think piercing is a must-have, or that it would solve every issue they have with range or power, but it would at least alleviate them, and it had no reason to go away (unless there was something else to it as a mechanic, we all know Marisa's options are kind of janky and mess up on replays sometimes).
Also Reisen's piercing in LoLK is pretty useless, as well. XD
She kills Sagume a bit faster than everyone else but still lol
Marisa just straight up murders all of Sagume except her last spell, but Reisen's piercing gives her a slight damage boost on Junko because of her larger hitbox, much like UFOMarisaA with Byakuren