We don't really know that the secondary hull would do any good in emergency separation. Sure, some TOS references suggest there's plenty of life support capacity down there, possibly including Kirk's cabin in the early episodes. But the cavernous cargo hold in TMP might have done away with much of that. And neither TOS nor TMP gave the secondary hull impulse capabilities, any more than the saucer got warp capabilities.
Doesn't mean there wouldn't be a need for docking ports in both halves in a separation emergency. In a real hurry, it would be way too clumsy to unpark any shuttles from the hangar and use them for shuttling between the hulls, but a slower-paced emergency might benefit from this. And perhaps the ports can handle the unseen but signage-verified lifepods, so that a partially loaded pod can be docked after launch and stuffed with more refugees? Having the docking port right next to the lifepod stations (just like Probert's matte interior suggests) would be helpful there.
We don't know if a docking port can mate with another docking port. It doesn't look like a symmetrical system at all, but we might be mistaken, and the saucer might dock with the secondary hull after separation. Alas, the saucer has no ports capable of reaching any of the secondary hull ports, but still...