There have been many interpretations as to what these markings represent, and the topic has brought forth many lively discussions. Someone even suggested the color, shape and arrangement of the markings on the underside of the engineering hull could represent some kind of Starfleet code. Don't ask me to explain, it's just one of the ideas that was tossed around.
A possible clue as to what these markings are, may be found in their location. Most of them are on the bottom of each hull.
With this thought in mind, what is usually located at or near the bottom of passenger planes, Greyhound busses, train coaches, cruise ships and motorhomes? Cargo storage areas, of course. Now, is there any reason why the location of cargo holds would be different on a starship? Off hand, I can't think of any.
Regardless of who's deck layout you agree with, you can't deny the fact that a starship is going to be carrying cargo, and the most likely place for that cargo to be stored would be in the lower levels of the ship or hull. That means there must be some way of getting the cargo in and out of that area.
So, since cargo holds are at the bottom of the hull, and the markings are also at or near the bottom of the hulls, it would seem likely that one or two of them would be cargo hatches.
That seems like a logical argument, right? Wait a minute, now! This is the 23rd century we're talking about! I'm sure those cargo holds have transporters for beaming that cargo to and from the ship. Sure would save a lot of grunt work. Just use anti-gravs to move the cargo on and off the transporter. So, why would you need cargo hatches?