Inputting a move once will add it to the Stale Queue at most once.
After multiple tests, I can confirm that a single thrown Holy Cross will be added to the Stale Queue a single time if it hits someone--regardless of how many times it hits or how many people it hits. It deals more damage when it's going away from the Belmont and less when it's coming back, but on the way out, it'll deal
8.4% -> 7.3% -> 6.6% -> ...1.
Here I've tested that with 3 menacing Simon's:
And here they are getting hit2 (click for a larger image):
And here is me hitting a single Simon right at the edge of the Cross's range so it'll only hit once3:
As you can see, both iterations have the same damage outputs, meaning that a move can't be put into the queue more than once if it's used only once.
So while the Holy Cross works as expected, the Holy Water is actually a little special...
Items don't stale.
As has been the case since Smash 4, items don't stale. This makes sense, since the whole purpose of items like a giant hammer are to hit people repeatedly. But what gets interesting is that moves from characters that produce something grab-able are usually considered items. So things like Mega Man's Metal Blade, Peach's turnips, Link's bomb, etc. are still added to the move queue, but they'll all deal the same damage no matter how often they're used--meaning characters with a special like this can freely refresh all of their moves by filling their queue with an un-stale-able special!
Now if you didn't know, it's actually possible to catch the vial of holy water that the Belmont's throw! If you're looking to test this, I'd suggest using Isabelle or Villager to Pocket the vial with their Neutral-Special and then use Neutral-Special again to bring it out and hold it for you to examine.
Because its grab-able--much to my surprise--the Belmont's holy water counts as an item! As such, it won't stale at all. Being hit by the vial will always deal 3.4% and each hit of the flame will deal 1.6%1.
1. Note that in Smash Ultimate, damage and knockback are adjusted for a 1v1 fight. These are not 1v1 values, so while they'll be true in a team battle, the numbers will be 1.2x higher in 1v1.
2. Ignore the differing percents on the Simon's, one of them got up a little too early and so didn't get hit with the Cross coming back. Look at the Damage box on the right for the value of the last bit of damage a CPU took.
3. I was forced to bring another Simon in to stand in the back to prevent being bumped up to 1v1 damage. See  for more.