I like pauses. Disconnects or some weird bugs can always happen and it is nice that pauses enable teams to deal with these issues even when in-game.
Pauses can cause other issues, like already mentioned, ship respawning during a pause or that the pause ends with clouds bringing one team into a disadvantageous position. Both of these could be prevented by a ref simply not allowing a pause when one ship is dead or not unpausing immediately when a team is in a more disadvantageous because of clouds. It may just be me, but I have a feeling that a lot refs don't really care about these kind of issues and just want to watch the teams kill each other, regardless of their current position, otherwise the refs would have addressed these issues to the organizers, I would imagine.
Refs have no power whatsoever to ensure that a pause is a pause, yes, but they also don't have the power over anything at all in reality. I don't see the ref's lack of ability a reason to remove a feature a tournament or event introduces, because you might as well not do the entire tournament or even to begin with for the very same reason. Really, nobody has to surrender or ready up when an invisible timer runs out, the teams just play along, all tournaments and events in GoIO are just a "gentlemen's agreement".
Refs also sometimes call pauses seemingly randomly and different refs don't always pause in the same scenarios. That is because of how simple the pause rules are. So, either trust your referee to know what's best or make your own impeccable pause ruleset for refs to use in the future.
Teams also don't instantly react to pauses and some teammembers don't read the chat. However, I do suppose it is fair to believe though that at least one out of eight people has the time to notice a change in the chat, while being outside of any engagements, and is able to tell his pilot about it via voice-chat who in return can tell his co-pilot. Although some time for teams to react should be calculated in by the ref when calling a pause.
I would also rather have an official pause than something that teams have to request from their enemy. I find it much better for players to have to deal with the ref following a very loose ruleset than for players to call other players mean names and accuse them of winning through "unmoral behaviour", when players start requesting for pauses in unacceptable situations, like when they are about to die.
Considering consequences, well, pauses are more of a convenience and the players themselves are responsible for being able to play on their own pc during the time of their match, so it is not wrong to say that it is their own fault, even when more than half of issues requiring a pause are out of people's control. I guess to make teams pay more attention to pauses they could be given a silly title when they failed to do so multiple times, like "Least Chat Attentive Team of the Week" or something, nothing mean of course, because that would be mean, although that example may already be mean, depending on oneself.
And if a ref doesn't respond at all, then the teams decide if they want to be nice and pause or just follow the rules of when a ref doesn't say anything, then the match continues normally. If the ref is not able to respond for multiple occasions, I imagine for the future it should be thought about replacing said ref or adding a secondary ref until the primary ref got his stuff back together.