I honestly don't know why they are there. I heard a story I hadn't been able to confirm that the dimples on the only long box E kits were there to help de-mold the part (kind of like ejector pin marks, but not flush with the saucer exterior). When they got to the small box retool, it looks to me like whomever tooled up the new kit interpreted the dimples literally and they became more of a kit feature (and were centered to the rest of the lower saucer details).
In a weird twist of fate, while I don't believe the dimples originally were a feature of the classic Enterprise, it seems they may have possibly inspired the docking ports on the Movie E. During the pre-production of Star Trek Phase 2, the studio model being built had at least one or two docking ports present on the lower secondary hull (below the 1701 markings on the bottom of the hull) where a Dodecahedron shaped travel pod would dock while the ship was in drydock. I've seen one painting that seemed to indicate there might have been a similar port planned for the lower saucer (perhaps more than one). One of the famous photos of the Phase II E studio model being built shows a primered small box 18" AMT Enterprise sitting on the table behind it presumably to provide some 3D detail inspiration. Of course that model was scrapped and the Motion Picture Enterprise was all new. But they kept in the travel pod sequence and there was at least one docking port on the lower saucer, but it was inside an airlock with a flush mounted door. This is the airlock that Spock and later Kirk used for their V'Ger spacewalks (both in the cut version and the scene that appeared in the theatrical cut of the film).
