It's not clear from your code what relationship there is between inpoly, a logical array based on the data in one file and the list of all files. Assuming that inpoly has equal or less elements than the list of files, you could use it to index that list as you have done, but are you sure that's really what you want to do?
Beside this, it's unclear why you have the same function call in two successive lines. It's going to return the same values each time. In addition, if you use a logical or | instead of + you don't need to bother converting back to logical and you certainly don't need 3 variables to do that
[inpoly ,onpoly] = inpolygon(lon,lat,lonv,latv); %don't need to do it twice
inpoly = inpoly | onpoly; %logical OR. inpoly stays logical, no need for ind, or ind_logical
latout = [latout; lat(inpoly)];
lonout = [lonout; lon(inpoly)];
However, note that as documented, inpoly also includes onpoly, so even the logical or is not needed:
inpoly = inpolygon(lon, lat, lonv, latv); %inpoly also includes points ON the polygon
latout = [latout; lat(inpoly)];
lonout = [lonout; lon(inpoly)];
