Installing in both sims will not cause any problems. If it were, we would clearly advise it or, likely, prevent the installation under P3D if FSX was found.
If both FSX and P3D are on the same system, you just need to be a bit careful when *uninstalling* because, the uninstaller entry will be only one, but will actually uninstall the version installed last so, if you would do a complete uninstall on BOTH sims, you would need to
1) uninstall from P3D, then reinstall into FSX and uninstall from FSX, if you installed on FSX first
OR
2) uninstall from FSX, then reinstall into P3D and uninstall from P3D, if you installed on P3D first