Ok, here's my opinion on your list. You'll note that I hate hard-and-fast rules as much as possible, and would much prefer social pressures.
1) The key distinction to make is between useful bots that provide a service or do something unique and not annoying, and useless bots that provide repeat services or don't really do anything. There really aren't that many bots at the moment. (Ok, I wrote that line before I actually went through the list. But you made it sound like everyone had a bot or two.) But here's the list as I see it, and their function:
- Mint: Provides japanese translation service, ping service, and several annoying and pointless kicks. Judgment: Needs some modification, but otherwise useful.
- Philia: Never speaks, and produces the piespy chart that people occasionally look at it. Given its lack of speaking, its only problem is it takes up a slot on the nicklist. If that's a problem, then... eh, find a new hobby. Judgment: Useful
- Ragnarok: Provides ChanServ type services. Has a few annoying kicks, but those may or may not be changeable, and really aren't that intrusive. Judgment: Useful, of course.
- Confeito: Experimental conversation bot. People weren't even supposed to know it's a bot. Anyway, you can ask me personally for more details on how it works. It has no true triggers, per se. Judgment: Who knows. It might start taking up too much RAM for me to keep it here.
- Chubbzilla (whatever his bot's name happens to be at the time): Doesn't say anything as far as I know. I think it provides something useful, though I don't know what. Judgment: Neutral.
- Hotaru: shuten's eggdrop. Doesn't really do anything as far as #eoff is concerned. So again, it's only a nicklist slot that's missing.
- Krabmeat: Not actually in there at the moment, but it's Cbc's. I don't think it does anything useful, other than let Cbc talk when I banned him overnight because I forgot to take it off. ^_^?
- Skwoo: I don't know what it does. Probably takes up a nick list slot. Oh noes.
2) As far as Munty's go, it's more of a protection scheme than anything else. A few months ago, we had a little protection war type thing in #waiting_bar, and the protections we came up with were somewhat elaborate. It got really bad in there, actually. I eventually wrote a script to just deop everyone except me. Oh, fun times. But anyway, they only affect trying to attack Munty's clones. They're pretty much useless scripts, though, but getting him to remove them (especially if they're buried in pages of scripts) may or may not be difficult. Ragnarok also has some mass-deop kicks, and I don't know what can be done about that.
3) Yes, the caps flood, punctuation, and repetition kicks are pointless and stupid. Burn, burn, burn.
4) This goes back to useful vs. useless. At the very least, if a script doesn't provide useful content to the entire channel (but perhaps to a single person), it should respond with a notice. Most of my scripts did that back when I ran mIRC. That can result in trigger flooding, so private message or ctcp based triggers can be useful too. I had a little used one for my seen script back in the day.
5) Multiple names isn't really a problem except with some select people (especially FFChatters). But obviously, one person being on pretending to be three is kind of stupid. Just remember that there may be times when two siblings might be on from the same connection or something.
If there's anything else, I don't know what it is. I'm usually quite lax with what I let people do, and the only thing that can potentially annoy me is lots of kicking or instabanning.