One control scheme that's used nowadays is two joysticks, with one to control orientation (pitch/roll/yaw) and the other to control translation (up-down/left-right/forward-back). I usually map the left stick to translation, with twist working the up-down axis.

Takes a little getting used to, but is pretty intuitive, and gives nice smooth analogue axis for all 6DOF.

Dual joystick was a setup I used with Descent but also experienced in Mechwarrior arcade. Allows for more precise control then a single joystick with hat switch. Feels weird at first though!! Controller prices were a premium back then so keeping two joysticks in good working order was uncommon if you played hard.

The MS Sidewinder 3D Pro had twist to roll, throttle control for forward/backward, and a 4-way hat switch for translation (aka ‘strafing’, if we’re both taking about the same thing here). It was perfect for Descent.

Edit: and Freespace!

I played freespace long after its hayday. The mod loader was lovely and the mod community was still quite active. The most expansive overhaul mod had only one server that had many players. It was a full-on RP server. It wasn't for me, but it was fascinating nonetheless.

Don’t forget the Gravis Phoenix which was truly a high end joystick at that time and perfect for Descent.

Hmm... I need to try harder with hats, I've never felt great about using them.

The Space Orb was the most effective way to play D2 once you got used to it.