I'm playing Krastorio 2 Spaced Out, which has two tiers of night vision which are both 1x1 in the equipment grid. I believe the first tier uses the vanilla night vision equipment's prototype rather than hiding it and creating its own.

If I use the night vision toggle button, the disabled version is 2x2, and if it can't fit because the slots below and to the right of it are occupied or don't exist then it gets deleted.

I would expect the disabled version of any piece of equipment to be the same size, which means you'd need to check the size when creating the disabled copies. I haven't tested yet if the 2nd tier of night vision has the same problem, nor if it'd get replaced with the first tier upon reactivating it, but Personal Tesla Defense Equipment worked flawlessly with the toggle personal laser defense button.

I would also expect that any equipment change that is blocked should at least return the item to the player's/vehicle's inventory rather than deleting the item.