Wow thank you for this detailed response! I read every word. If my teachers taught this well I would have learned so much more in school.
Oddly enough, I actually had a 4-year gig as a private tutor at the college over here. Granted, the subject was Music - theory, lit, aural skills, class piano - but I guess I got decent at explaining stuff over the years.
The place had a lot of good teachers too, which is always a great start. I also had a bad one, but in the end you learn both what to do and what not to do, so I think they both ended up being for the best.
So if I made a dungeon as interior, could I stick one nes style room inside to have 3 bomable walls? Or would that not look right?
Actually this brings up another question I had.... In ALttP for example, the Overworld has many bombable walls. How would I be able to accomplish this? By splitting up my overworld into many small dmaps? and limiting the quest to one secret cave per dmap?
I'm not entirely sure what you're getting at...
...so let's start with ALttP. The ALttP overworld had a lot of bombable walls, but so does any Z1 overworld. I think you're getting at the fact that ALttP could have multiple bombable walls per section, while Z1 can only have 1 bombable wall per section? Z1 uses very small single-screen sections, while ALttP uses very large scrolling-screen sections, but they're all part of one single Overworld DMap (let's just carry Z1 terminology over to ALttP for now). So, changing any segment of your Z1 game to any variety of DMaps will never change the per screen limits, because those are... well, per screen, not per DMap.
I would imagine that the Z1 designers thought that, due to the small screen sizes, using a single secret state per screen would be enough. After all, 8x16 gives you 128 total overworld secrets. By contrast, the exponentially larger scrolling screen sizes used in ALttP would require an entirely different secret state system that supports multiple secrets per screen in order to allow for anywhere near the secret density of Z1. After all, the ALttP overworld only has 40 screens, despite being 3 times as big graphically. And if you bothered to calculate ratios, I'm sure you'd find Z1's overworld has a considerably larger secret density than ALttP's.
For now, I wouldn't count on an ALttP-style multi-secret-state system being implemented into ZC. It would be a total reconstruction of the current system, and then you'd have backward-compatibility problems on top of that. In fact, another thing to keep in mind is that the secret state refers to all secrets, not just specific kinds. I remember another user having a problem where they wanted a bomb secret and burn secret on the same screen. They would set the bomb, and it would blow up fine. Or they would burn the tree, and it would burn fine. But if they bombed the wall and left the screen, they'd come back to a bombed wall and a burnt tree, and if they burnt the tree and left the screen, they'd come back to a burnt tree and a bombed wall. You get one secret state per screen, no matter what flags you use.
(There are certain brands of sorcery that allow tiered secrets by way of combo cycling, but these are all temporary (see how they reset when he leaves the screen in the video), and they have no practical use in creating multiple bomb secrets.)
As for one NES Dungeon room with 3 bombable walls... if you want to bomb directly into the next room over, then you have to do like Jamian says and be sure each of the 3 rooms on the other side of the 3 bombable walls are also NES Dungeon rooms so that each of the "bombed wall" attributes carries over, or else you'll just get caught in a solid wall when you pass through the hole.
Alternatively, if you only want to make cave entrances, then keep in mind that you can construct your own Door Combo Sets. If you go to Quest -> Graphics -> Door Combo Sets, you can click the <New Door Combo Set> option and build your own. There are no graphical restrictions, so you can use whatever combos you want in whatever CSets you want. A Door Combo Set doesn't have to pass through to the next room over.
Just be aware, these apply to very specific areas of the walls:
The parts in gray/white are the only parts you can apply these sets to, so whether or not it would "look right," is up to you. Would 3 bombable walls in those precise positions look awkward or unnatural? Depends what kind of screen you're making.
If you decide to use these, the Door Combo Set editor can seem overwhelming. You get 10 possible states for each of the 4 walls. But if you're only making bombable walls, then you only need to design the "Wall" and "Bomb" sets - other functions that you aren't using, and other walls that you aren't using, you can leave blank.
In fact, this post gave me an opportunity to try something I've wanted to do for a while: take a blank room and make a bunch of whacked-out bomb sets. Check this out - bombing left reveals a cave with stairs and lever, bombing up shifts all the tile CSets, and bombing right turns the wall into a forest:
Because why not blow walls into rainbows and forests? And you can even use the lever to make a treasure chest appear (though it resets if you leave the room):
So like I said, there's no graphical restrictions. Functionally, the way the set operates remains the same: the center passage becomes a walk-through path that pulls Link into the wall and off the screen. Combo solidity and functionality are overridden: you'll walk straight through rocks and directly over tile warps and damage combos.
Still, if you don't want to pass through to the next room, you can set a Side Warp using the Entrance/Exit type and it'll take you to another room or map like any other entrance would. You could use that to enter your caves, but you wouldn't get the walk-down effect, so you'd have to design your entrances to look like they could be walked into instead of being a staircase.
Reading back over this unexpectedly long post, it's not anywhere as complicated as it may sound. I'm just trying to point out the possibilities - once you pick one, it should be short and straightforward.
I should probably just start writing wiki articles...