It is now possible to use date formaters in log filenames (in mask options).
For example to have log by year and month in separate directories, you can do :
/set logger.file.mask "%Y/%m/$plugin.$name.weechatlog"
You'll have a tree like that:
~/.weechat/ |- logs/ |- 2009/ |- 12/ | irc.server.freenode.weechatlog | irc.freenode.#weechat.weechatlog |- 2010/ |- 01/ | irc.server.freenode.weechatlog | irc.freenode.#weechat.weechatlog