The thing is, the reason people apply to a given college is often pretty random and you can't assume that it is a fully informed decision. If applicants have been to open days, they'll have picked a bunch of colleges to visit - tending to focus on the ones that are close to each other, or the ones that are the most famous. Most people won't make it over Magdalen Bridge as it's just a bit too far and the wrong end of town from the station. By the end of the day, it's all a bit of a blur but perhaps a particular college will stick in their minds as being pretty, or they particularly clicked with the student rep who showed them round. Lots of people don't even go to open days and are picking off the basis of website pictures. And so it's not surprising that the highest number of applications go to the big ancient rich colleges, which also have the fun facts about them that can give someone a reason to remember them (Magdalen has deer! Harry Potter was filmed in Christ Church!) And finally, richer colleges have more money to spend on outreach and that also boosts application numbers. Historically I think colleges earlier in the alphabet used to get more applications because before the internet, people got a brochure, and and didn't read all the way to the end!
So the reasons some colleges get more applications than others don't really tell you anything deep - they definitely don't mean the less oversubscribed college is 'worse'.
In the case of St Hilda's, it's also true that it went mixed sex much later than the others, and so parents/teachers may not realise it's co-ed now. And of course some people just want to apply somewhere with the ancient quad vibe - which no worse a reason than any other.
As you say, there are lots of great things about St Hilda's. It's on the river, beautiful grounds, Jacqueline du Pres building is an excellent music/theatre venue, close to Cowley Road, close to University sports facilities and swimming pool.
In practice students always end up thinking their college is the best, even if it's not the one they applied to