Ok, just went back to the codex and it seems I was wrong. Apparently, most frigate sized ships and smaller can land on earth-like planets (source):
Frigates are light escort and scouting vessels. They often have extensive GARDIAN systems to provide anti-fighter screening for capital ships, and carry a squad of marines for security and groundside duty. Unlike larger vessels, frigates are able to land on planets.
In fact, I am also remembering now that in Revelation, the SSV Hastings landed on Sidon to deploy Lt. Anderson and his team. The SSV Iwo Jima entered the atmosphere of Camala to pick up Kahlee Sanders and her extraction team but was destroyed before she could land. Both were standard frigates for all we know.
So I guess there should be spaceports for ships of that size.
As for the Normandy in the beginning of ME3, don't they say that she was in "dry dock" to get the retrofit (which is not quite finished when we get on board)? I always assumed that Vancouver had some sort of military docks and construction facilities near the HQ where Shepard is being held,