This should work:
ex:=\sin(x)**2+\cos(x)**2;
map_mma(ex, "Simplify");
and produce "1".
If it does not, something has gone wrong when building Cadabra with Mathematica support. It is possible that your version of Mathematica is too new and was not picked up when you ran cmake -DENABLE_MATHEMATICA=ON ..
. Try pulling from github; I have just pushed a change which includes an updated FindMathematica.cmake
script.
If that still does not work, send me the output of that cmake run by email and I'll have a look.