Yeah, probably! Dipper and Mabel are both leaders in their own ways and, I’m not sure how individual the Prefect selection is per House, but I think they’d be good examples of the positive qualities their Houses reflect and good role models for the other kids to look up to!
[I do however think Dipper and Mabel would be the kids that sometimes sneak out after curfew, which Prefects aren’t really supposed to do (heh they’re supposed to stop the kids who are out after curfew), but I think the mystery twins would mostly do it for heroic purposes. Sometimes for their own reasons, to meet up with a friend or, in Dip’s case, study forbidden spells and stuff, but it wouldn’t be all the time (and contrary to what you'd probably think, Dipper would be the one who does it more often than Mabel).]
Mabel would be a pretty chill and super friendly Prefect for Hufflepuff as far as rule breaking goes. She’d step in if bullying was happening or someone’s safety was on the line, but other than that I think she’d encourage as much fun and friendly interaction as possible. She’d be especially lenient toward romantic couples that she catches after curfew, probably tellin those ‘crazy kids’ to run along and try not to let her ‘catch ‘em in the halls next time’. She’d be super excited at the beginning of every new school year because the little first years are so adorable and she loves getting to meet them and show them around to their dorms and ease their worries. When there’s bad weather over breaks, she has all kinds of fun games and crafts for the younger kids to do. I also definitely believe Mabel would encourage as much interhouse mingling as possible. She’d totally be against prejudice and fight for equal treatment between all Houses because everyone has the potential to be a wonderful person.
I think Dipper would be a pretty chill Prefect for Slytherin too, but not for the reasons that Mabel is. More like 'I don’t wanna be known as a stick in the mud especially if Wendy is still going to this school for another year hey you guys should totally pass the message along that I’m the COOL Prefect. because I am. I’m cool. Now you kids run along and stay out of trouble okay’ unless he knew from past experience that the kids were definitely troublemakers and could threaten his Prefect status OR he caught people he didn’t like from his House breaking the rules, like Gideon. Then he’d happily and smugly issue a detention and order them to march their asses back to the dorms. Like Mabel, Dip wouldn’t tolerate physical harassment or bullying either.
[I really like the idea of Dipper being upset to be sorted into Slytherin at first because he really thought he was going to be in Ravenclaw or Gryffindor, Grunkle Stan was a Slytherin, and all he knows are House stereotypes. But gradually he begins to see that those stereotypes are wrong and yeah maybe there are some bad kids but there’s bad kids in every House and he can relate to these nicer intelligent Slytherin kids that are condemned and misunderstood before people even get to know them (some that didn’t even have a choice about how they acted because of their parents, like Pacifica) so he pretty much makes it his civic duty to fight for justice and prove that Slytherin House isn’t full of bad people. its just people that want to be treated better.]
So during Dip's first year as a Prefect he's really nervous about meeting all the new kids at the beginning of the school year, but then he sees how nervous they all are and maybe upset they are to be placed into Slytherin. he sees himself in these kids so he pulls them aside and assures them that being sorted into Slytherin is nothing to be ashamed of and they’re going to fit in just fine around here. he’ll make sure of it.