I'm not familiar with the bnccheck stuff dZSbot does. It shouldn't be a big thing to allow disabling recording of logins, however I'm not convinced that's the best solution. I would guess it makes more sense to enable/disable whatever the bot is doing in the bot itself. I can understand the problem of cluttering up the logfile with lots of login/logout events though.
SQLite is indeed a possible solution however it's best applied to the userfiles and not logfiles. I don't think scanning logfiles to find entries for !nuke/etc makes any sense for some of the reasons you just pointed out as problems. That's what a directory DB like that maintained by nxTools is for.
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