I don't have multiples, but if I did I would definitely separate them.
All the twins I went to school with were in separate classes from the very first day. Having siblings in the same class was an unheard of concept.
DS will be in grade 5 this year and he has a set of identical twin girls in his year. Their mother is a teacher at the school and has insisted that the girls be kept together every year thus far.
As an observer I personally think this a disservice to both the girls and their classmates, for quite a few reasons. Firstly, the girls are almost treated as one unit. Uniforms are worn at our school so there's no distinction due to clothes. They both wear the same hairstyle, instead of one in, say, plaits and the other in pigtails. Interestingly, on free dress days they wear very different clothes so I suspect it's the mother who has the issue with letting them separate moreso than the girls.
They seem to spend a lot of their time correcting people as to their names, and seem very codependent. At a birthday party for their very close friend, Twin 1 spent her time in tears because Twin 2 was at home sick. The twins had spent lots of time with their friend and her family over the years and the twins' father was there, so it wasn't as though she was all on her lonseome amongst strangers, but because Twin 2 wasn't there Twin 1 was basically falling apart. It was a very sad indication of their codependence.
The other thing I've observed with these girls over the years is that the teachers often feel obliged to keep things 'equal' between them. If one gets a classroom helper award one week, the other will the following week. This is really unfair to the other kids in the class as they are missing out on awards/recognition, just so one sibling doesn't feel left out.
More than once I've overheard one of their classmates say that no one needs to bother trying for the classroom award next week as they already know that Twin 2 will be getting it. Plus, if I was one of those girls, I'd wonder if I had really deserved that award/recognition, or whether it was just given to me to keep things 'fair'.
They usually get similar marks/excel in the same subjects, but the one time they didn't, the mother was most put out that the second girl didn't get an award, and of course the twin who missed out was upset wondering why she didn't get an award when her sister did. The one getting the award felt guilty for doing so. It was a real mess.
Despite this they are lovely girls, but the longer it's left, the harder it will be when they DO have to go their separate ways.