There's already a system variable for number of uses of an item.
$ITEMUSED1
Each item has a number beside it (which is what the number beside 'used' correlates with). Each time you use the item, the variable gets 1 added to it (so if you used it twice in the game, it would be at 2).
You'd have to use the item script of that item, to do a check when you use it, and if the $ITEMUSED1 value is equal to the limit, change the destination they go to, to some default "there is no more uses".
Unfortunately, there's no "disabling" an item or something.
Of course, when you reach the limit you could always replace the item with an item that looks the same, but has no links to anywhere (and it's description says it can't be used anymore). Then, when they "replenish" the item, switch it back to the old item (and reset $ITEMUSED1 to 0).