I went with option three as personally I prefer larger buildings even if it isn't practical or necessary to explore all of them.
There is the problem of actually filling the rooms and having enough interesting things to find, but I don't think they all need to be used for anything significant or have that many good things to find. I think if there are ways to provide the player with some idea of where certain items and types of items are then players can use that to narrow down their search.
When you go into your average building you don't search every single room to find what you want. Most buildings or facilities start with a room where you are provided with some information as to where you should be going in order to get to your destination. In an office or school there will be a list of floors and room numbers catagorizing rooms by purpose, in the case of an inn or hotel then there will be information regarding who is, or in this case was, using which room, and so on and so forth. This can apply to entry into abandoned buildings or less than legal entry into buildings that are operating, it seems reasonable that a thief or looter would have some idea of where the valuable goodies are before trying to brute force search through an entire building and places that are more likely to contain such valuables, like vaults or storage areas, would be good places to start searching.
If you have some idea of what you are looking for and where it might be you can eliminate much the need to brute force search each and every room. Things like old documents regarding the contents of a building and which rooms they are in (floors 32-35 belonged to a certain department), clues seen from outside the building (why are all those vines growing out of that one window?), information regarding what the room was used for (there is a safe in the basement), information from NPCs (I hid some valuable X somewhere on the third floor of that building), tendencies of certain items to be in certain kinds of rooms eventually learned from experience (items of this kind tend to be found in these kinds of rooms), and things like that can be used to narrow down the player's search according to what they are looking for.
Say for example you know that magical item X causes certain things to happen to the area around it, maybe it emits light, attracts bats, makes vines grow out of it, or something like that. That's something you can use to attempt to locate it. If I see bats flying around a certain window or door, light coming out of it at night, or vines growing out of it, then I would be entering the building with some idea of where to look for something nice. There may be other goodies in the same building, but I don't have any info on them and if the building is to big for me to be practical to search every room within a reasonable time frame then that in itself would keep me from attempting to go for such goodies, at least until I know more about their whereabouts.
If I'm looking for tools then I would look in a room that would have housed tools. I enter a building and see from the sign that the workshop is in the the second basement, so I go down to the second basement to find the tools. Again, there may be other goodies in the building, but unless the building is small enough for me to search all the way through I'll have to make the call whether or not to stay look them or clues about where they might be.
Say for example I need a certain substance from a certain creature that I know needs an easy source of water to make its home. I would then be looking for places with water, such as bathrooms, mechanical rooms, boiler rooms, and the like. If such a creature is consistently placed in such rooms then the player can eventually learn where to look first when seeking them out.
What if I find that a school has a chemistry lab. That chemistry lab may have some nice ingredients for crafting and would be something I would prioritize as I search the building for any good loot. Again, if certain ingredients, in this case certain chemicals, consistently appeared and/or are more likely to appear in such rooms then the player can use that to find what they are looking for.
I think it would be interesting if finding information about what a building may contain and where the interesting loot might be can be a part of the game.