No, it would work fine. That's why you're using $network if you use the on CONNECT event and if you're setting the nick through /server, then you're already setting it to the right connection. All events work on the connection that the event is triggered on, no matter how many connections you have. For example, If you were in the same channel on two different networks, if you have an on TEXT event and it triggers, it will affect the network it is triggered on instead of other networks. And so on.
Here's an example of using on CONNECT. You can, of course add additional things like your alternate nick or have it set the nick using $readini() if you store the information in an INI file instead of in the script itself or any number of other things.
on *:connect: {
if ($network == Undernet) { nick UndernetNick }
elseif ($network == Efnet) { nick EfnetNick }
}
scon and scid are mostly for doing things on a network that didn't trigger the event (or all networks). If you're just doing something on the network that triggered the event, even if you want something done on many networks when they each trigger the event, then you don't need scon or scid.