STGs? I'm pre-coffee and can't figure out what this stands for.
It's relatively easy to put out a new Drpg on an existing engine if you want to. Fans tend to be fairly forgiving of stuff like reusing art assets (hi SMT!) if it means getting new games in a niche genre. Code in a few new systems, design some dungeons, and... game. I'm not saying it's simple, but it is fairly low budget if you want it to be.
i haven't researched any specific apps, but found this thread for you:
http://forum.rpg.net/showthread.php?570053-iPad-good-mapmaking-apps
I see apps like DM Cartographer and PenUltimate mentioned. Maybe more, need to read the thread later.
Evil but brilliant.
Grid paper already has all the lines, so you're just drawing really short lines to make them dark every step where walls are, and occasionally making marks to designate ladders/traps/etc.
The real trick is dealing with spinners, teleport traps, pits, darkness traps, and other nasty things that intentionally try to get you lost and or mis-mapping (by teleporting you to identical but different hallways, for example)
Like this.
Which game are you talking about in the first paragraph?
As for the last paragraph, I know some people take screen shots of the map.
That's pretty much how I feel about them, too.
The issue with dungeons in oreshika for me was also something awesome about them -- they weren't floors, but a totally intertwining number of tunnels, where you could easily go over/under (often even seeing them) other, older or un-discovered paths. It could be very hard to follow, and it would also be pretty hard to map.
the time limits in Oreshika didn't bother me at all, but I find Atelier unplayable due to time constraints. It's because the time limits in Oreshika aren't 'game breakers'. if you fail one year, just try next year, and you have infinite tries. And if a goal is particularly deep in a dungeon, you can just leave a month or two early to make sure you get to it on time. Atelier has a game timer, and that makes me feel like every action is wasteful.
RE: last paragraph... the original Wizardrys are perhaps the most cruel maps of all time. Then again, most drpgs/crpgs of the 80s were vicious. That was back when most of us bought a game and played it for months (or longer) and so hard, viscous games were par for the course.