A little optimizing.

#csprot on
on @*:JOIN:#php.is:whois $nick | .enable #WhoisHide
; ^^ No need for the ! (not me) prefix here, you can never be opped when you join a channel.

#csprot end
#WhoisHide off
raw 319:*:{
if ($istok($3-,#counter-strike.is,32)) && ($istok($3-,#php.is,32)) {
;^^ No need for $lower() $*tok identifiers are case insensitive by default.
msg #php.is Counter-Striker alert! ( $+ $2 $+ )
}
halt
}
raw 311:*:halt
raw 307:*:halt
raw 308:*:halt
raw 309:*:halt
raw 310:*:halt
raw 313:*:halt
raw 317:*:halt
raw 312:*:halt
raw 301:*:halt
raw 318:.disable #WhoisHide | halt
#WhoisHide end
$istokcs is the case sensitive version of $istok, same for the ther $*tok's dealing with strings.