How would the UK leaving the EU affect academia and PhD admission?
The following are opinion, not fact, as AFAIK nobody has a clue what a potential post-Brexit academic situation would look like:


It's standard for qualitative features in regulations and costs to remain fixed for students over the lifetime of their studies. So I would guess that the fees won't change halfway through: you'll know the approximate costs at the start. It wouldn't surprise me if in two years fees for EU students would remain the same, especially if (as your question seems to imply) you've been normally resident in the UK for 3 years.
I would always expect a PhD studentship to cover fees. I would be very wary of one that didn't guarantee this. The risk of higher fees should be on the studentship, not on you personally. (Of course, you may self-fund, which is a different issue)
In the current UK climate I would be more worried about visas to study. With the current arguments around net migration, and the crazy situation where students are counted as immigrants, I would expect student visas from the EU to become a problem.