Inside your inner for loop, you read three .nc files. For efficiency, you need to reduce the number of files you need. So reverse the order of your loops
for j = 1 : N3
FileNC=P{j}
ncdisp(FileNC);
latidudine = ncread(FileNC, 'lat');
longitudine = ncread(FileNC, 'lon');
umidata = ncread(FileNC, 'ssm');
do the two find and through to sm=sm*0.5
for k = 1 : N1
LAT = Latitudine_stazioni(k,1);
LONG = Lognitudine_stazioni(k,1);
[val1,idx1] = min(abs(Long-LONG));
and through to the end of your loop, to the assigment to SM(j,k)
end
end
