So, does that mean the city is going to stop constantly rejecting permits/approvals for places to be open late?

Because that's what's been happening to date.

I don't see much merit in the ruling or proposed remedy.

The judge being frequently out of step with his colleagues is quite notable, as it's a bunch of his colleagues that will decide an appeal. If they all ruled pretty similarly, we could say it's unlikely for an appeal to succeed. If one guy is frequently way out of line with the views of others - it's much more likely for his decisions to get overturned on appeal.

There's plenty of basis for the ruling to be overturned, he's generally an outlier in terms of opinions.

The judge in question was pretty much expected to rule this way, and it's pretty likely it'll be overturned on appeal.

He directed them to examine re-scheduling it. That's about as close as he can get to an order, and I imagine they will probably do it/go through the process to do it.