Is there a stacking limit to how many Presence can be in a land? Can a large stack count as more than one Sacred Site?

Is there a stacking limit to how many Presence can be in a land? Can a large stack count as more than one Sacred Site?

No, you can have as many Presence disks as you want in a land, but it can only count as one Sacred Site.
More generally, there is no stacking limit for any piece in the game unless an Adversary or Scenario adds one. (However, there is usually no benefit to having more than 2 Presence in a land, unless you expect to lose some of it shortly.)