because the audience you claim to be targeted by those very little niche titles could very well be already on the console, considering how much it sold in the nowaday Japanese market, the sales that the big hitters got, and the presence of fewer but still present titles targeting a similar audience
It is a matter of size of target audiences: it is way more probable that the very small group targeted by "niche titles" also has a 3DS than due to one of the many way bigger titles, than not or viceversa.
It's logic and statistics.
Let's take for example the VIsual Novel genre, targeted by various small VIta titles. It could very well be that Ace Attorney series is of interest for that target market group and, being it able to sell way more copies than a small niche VN title on Vita, we can assume that a vast portion of that target group is already/also a 3DS owner.
We are not talking about a large enough group/genre of big enough sellers to presume that the niche target group isn't already present on the 3DS market
It is not that we have a big seller genre/title selling hotcakes of Vita to presume that the 3DS is missing out on that group, unlike it was for the cooperative action genre in Japan with Monster Hunter back in the PSP vs DS days, for example.
FAKE EDIT: now that I think about it, there is a title big enough on VIta and missing on 3DS that could lead us in saying that the 3DS is missing out on a particular target group, even if that target group is SO close to the classic and usual Nintendo core target group that I still think that the aformentioned analysis is still valid.
I'm talking about Minecraft