Overall I think pauses are necessary, but whether they are official or unofficial really depends. How would they function if they weren't official? Team captain only, or anyone on the opposing team? Is there a possibility for the opposing team to not go along with the pause?
Official pauses are kind of nice, in that they "can't" be ignored (according the rules). The ref also does a quick check to make sure the pause is valid (usually making sure a player is actually missing on one of the teams from a disconnect/crash). This makes it slightly less likely for a team to call a pause abusively. The ref can also make sure teams aren't engaged (and preferably not about to engage). Official pauses also have a time limit, to make sure the game keeps moving and everyone isn't waiting around 5+ minutes for a player who's just having a really bad day with their connection.
For unofficial, it might be a little faster in the call. When it comes to official pauses, someone has to request it, then the ref has to actually call the pause. Then they have to say they're ready for an unpause, the ref checks if the other team is ready, and the pause is off. It's quite an annoying series of steps, especially if you have a ref that's not paying attention or a little slow, or even on a little power trip. So unofficial pauses might start and stop faster, rather than a potentially significant delay from the request to the pause/unpause.
In unofficial pauses, you still have all the problems of an official pause (minus the disqualifications, which I haven't seen happen); people buffing, loading up ammo, etc. You can't pause clouds/ships, but I also don't think Muse will ever put something like that into a game, even if it does support competitive play a lot. (Maybe we could convince of a vote-pause option?) It sounds easy to just tell everyone to 'get a better connection scrub', but is that the kind of competitive community we want to support? For more competitive tournaments, I could see having no official pauses, but the SCS is more of a casual-competitive scene that supports teams of all skill level (and connection quality).
Personally I think the official pause is a little better. Even if teams try for a gentlemen's agreement, some teams just won't allow the other team to pause if they feel they have an advantage. When official pauses get screwy, it's usual a referee issue. Having refs paying attention to the match, checking the chat, not tabbing out, and making sure it's not just a moving cloud preventing a pause before calling it.