Maybe that depends on the local camara but I think in most areas internal wall changes don't need permission. I went to see the planning department in Ansiao to see what licences I may need and the knocking down of my internal walls were of no interest to them.
It's best to check with the Engineers department of your local Camara, as travis2 says not all have the same outlook, you might also have to inform Financas if it affects the rooms and their usage and therefore the formula used to work out patrimonial figure that IMI is bases on.
Don't forget to apply for the exemption.
I think we also had another bit of luck today....... whilst we were doing the paperwork, I noticed that the whole of the main building which consists of house, long barn and a double garage on the end are all registered as dwelling rather than dwelling and animal shelter/barn etc......... So I assume that probably means we can convert (at least) part of the barn into guest accommodation.