Just keep in mind that with the NiMH route vs the 2x18650 route:
-you will need an expensive battery holder
-you use three times more cells. Sooner or later one of them is going to fail... turning the entire pack obsolete.
-you need two 4-slot chargers to charge the cells (if you charge them out of the holder)
With the 18650 route you only need a simple, cheap, home-made spacer, you only use 2 cells and you only need 1 charger. If one of the cells goes bad, you just dump that cell, buy two new and use the remainder in your single-cell lights.
Also consider the size of spare packs and ease of use when switching packs. With 6xAA you either carry around 6 spare cells that you need to install in the holder when the other pack is empty or you carry around a huge cylinder with a spare pack: 32mm round x120mm
Two 18650's can be carried around very nicely in a box of 40x20x70mm and contrary to the 6xNiMH route you can switch them out in the dark.
Not so long ago I used to have two sets of 9x NiMH for my Mag85 / Mag3xP7 and one set of 3x DX 26500. Now these NiMH sets are having all kinds of trouble. Some cells have a very high self-discharge, others only hold just over half their original charge while others have a very high internal resistance.
I say the cost savings of the NiMH cells don't weigh up against the cost of the holder and my time. If I had to start all over I would definitely go for the 18650 route.
Not sure why you believe that 6xAA charging is such a hassle. There are several Maha 8-channel chargers that can handle the entire set of cells in one shot. Or you can use a hobby charger to charge the cells while they stay in the holder. Sure, if you don't have the equipment, it'll cost money to get it. But the same holds for Li-ion charging.
A 6AA -> 2D holder, such as from mdocod, is relatively expensive at around $40. But you don't have to ditch the entire pack if one cell goes bad. It's just a holder. You load individual AA cells in the holder. If one cell goes bad, you simply pull it out and put in a replacement cell. This is probably the main difference vs. using 2xLi-ion. Li-ions probably don't need a fancy holder. If you use 2x18650s or 2x26650s, you will need to make a spacer since the D Mag tube diameter is around 34mm ID. You will also most likely need to do a tailcap/tailspring mod to fit the longer cells.
Ease of use in switching AA packs is similarly simple. Remove the spent holder, replace with a fresh, loaded holder.
IMO, the choice of NiMH vs Li-ion could hinge on things like which bulb you plan to use, and hence the current draw and bulb voltage that the cells have to be able to handle, if you need good battery shelf life, and what run time you desire.
For the 5761, Lux Luthor's data shows that the bulb most likely will flash at less than 8.0V, which probably makes 2xLi-ion the wrong choice. If you were going to run a Welch-Allyn 1111, on the other hand, then 2xLi-ion probably is fine (unless they are 2xIMR26500 or larger, making flashing the bulb more likely -- here parasitic resistance in your flashlight can help to protect the bulb from instaflash).
A 5761 draws over 5A, so your AA NiMH cells better be good ones that can deliver the current and hold their voltage under load.
For run time, 6xAA NIMH could hold around 13Wh, vs say at least 20Wh for 2x18650. So you might get 50% longer run time with the Li-ions, if their Vbatt is compatible with the Vbulb you need.
Now if you take the JimmyM regulated incandescent route, then I'd say that Li-ions are definitely the way to go. I'd look into some of the various IMR26650 cells or the e-cig IMR26500s. A simple PVC conduit spacer is all you need to fit these cells in the D Mag tube. With the IMR26500s, a small tail spring trim and sinking the spring at the bottom of the tail cap will let you fit the cells. With the JimmyM driver, there is no concern about matching Vbatt to Vbulb to avoid flashing the filament. So load up the battery configuration to maximize your run time, set the JimmyM driver to the appropriate Vbulb value, and off you go.