The curvature of the dome bubble often acts as an additional lens, in front of the standard camera lens, and can certainly affect focus, especially with longer lenses where the depth-of-field is razor-thin to begin with (that is, it's more likely to be a problem at 50mm than at 5mm).
Last time I installed an Arecont dome, they included a little plastic piece that snapped on the front of the lens to simulate the plastic of the bubble and aid in proper focusing. Short of that, I find it usually work alright to hold the bubble up in front of the lens while focusing.
Of course, cameras with autofocus or ABF avoid the problem entirely...
Agree with Matt on last part. In last few years many fixed minidome cameras now come with features to locally or remotely focus the camera with the bubble on but before these came along i was taught same trick that works pretty well. It takes two hands but after focusing the camera, flip the bubble around so that outside center of bubble is up against camera lens then focus the lens. Flip the bubble around and install it. Worked very on analog cameras but will require more patience on IP cameras.