JOIN isn't a raw, it's just
:nick!user@host JOIN :#channel
that triggers the On JOIN event.
Currently it's not possible to hide or minimize channel window as they are open.
The only way to get around this, though, is by sending the command
/join -n #channel by yourself, so that the channel will be open minimized.
If, for example, you are being forced to join #chat on connect, use:
On *:connect: if $network == Lamenet { join -n #chat }
On me:*:join:#chat: .raw part #chat