Barely. For H3 maps you need to manually check any instance where object ID’s can be used. And there are a lot of such cases. Creatures/banks are the most obvious but you also need to check all armies, seer hut/quest guards, events…
Theoretically won’t be a problem with RMG but it is still in unfinished state.
There is one huge problem: updates. If mod with such creature got update you must trace all places where such creatures are in use. It may also trigger for H3 creatures in case if we’ll update something in config file (e.g. missing ability)
You can’t. When mod is not loaded/disabled VCMI will not load files from it at all.
Alternative solution would be possibility to mark all objects as “special” similar to current fields in creature and hero configs: object will not appear in-game randomly but still can appear if placed manually.
In this case there won’t be need to disable mod itself - just add small mod that will add or remove “special” : true from all objects.