I think it would be the most intuitive to have maps based on distinct areas. Distinct as in, naturally continuous areas, and/or areas that are named as part of the same area, especially if they are named as such in-game.
Like you say, Zelda maps should typically have an entire dungeon as one map. After all, maps show how everything is connected and relative to each other, maps for each room are not as helpful.
Very early on, Peardian sent in maps of
Super Mario RPG: Legend Of The Seven Stars as individual rooms, but has long since been redone by Peardian into logical areas. Though the latter is an incredible improvement, I was still happy to have the former at the time. I lean on the side of having more content, so I generally don't reject maps if they do come in individual rooms, even if obviously having them combined is preferred.
Not that I just accept anything; I have rejected maps that were individual screenshots of no value (and even been called out for putting one up because I barely even looked at it and didn't think about it much before publishing it). More to the point here, I once rejected Super Metroid maps that someone sent in, even though this was long before we finally got
Rick Brun's awesome maps. The maps I got were individual rooms, or if I recall correctly,
fragments of rooms, and instead of logical filenames they were all hexadecimal numbers. Presumably these "maps" were just the output from disassembling the game via a hack or editor, so whatever effort that took was negated by the lack of providing meaning to room chunks named "0C" or "F3" or whatever. Yes, I DO often rename maps before putting them up, to fit how previous maps have been named, but I'm not about to do research on hundreds of chunks because the "mapper" couldn't be bothered to.
I suspect this topic is a response to Lüt's submission of
Lunar: Eternal Blue on the Sega CD yesterday, since that's 790 maps all at once? I like both the marked and unmarked maps. (Yes, I plan to remove the excessive "(Unmarked)" tags soon, which I mass-added in the first place.) Could the unmarked maps be combined just like the marked ones are? I'll leave that up to Lüt... To his credit, he provided the table for the map listing (not necessary, often not even encouraged, but this is a lot of maps), and though I ended up doing some rearranging (like moving the marked maps first and in the "main" column), it would have actually been more work to deliberately exclude anything. Again, not that I would, as someone might find use for individual rooms, and since many of them are animated, they might actually work better if you're appreciating these images as they are as opposed to just using them for navigation.
TL;DR: The short answer is that these are MAPS, so rooms SHOULD be connected (but I might not reject them if they're not).
