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