Often the engine has a slight nose-up orientation because it's aligned to the local flow for cruise conditions.
If you assume a near-zero AoA at cruise, with the fuselage level, then the downwash behind the wing will mean that the local flow there is angled down. So to minimize engine drag its best to align the nacelle with the flow i.e. slightly nose-up/tail-down.
Still, the thrustline of a sidemounted engine is often closer to the cg (albeit above) than a podded engine's, and sometimes the magnitude of the nose-up moment from the latter may be a design issue.