I am pondering the same question and after some hours research I am still not wiser. I really need input from people who tested BOTH joysticks.
To me it looks, in simple words, the Hotas X of course has the throttle but the 16000m is "more precise".
* What disadvantage would the Hotas X have seeing that people say it's less precise?
* What disadvantage would it have NOT have a throttle/HOTAS and choose a joystick only, the 16000m?
Looking at it that way I can see me throttling either via keyboard or XBOX controller and then just use the "better " joystick 16000m? Why would that not work and why would a separate throttle like with the Hotas X be better?
The "more-precision" argument is based on the fact that hall-effect sensing (T16000M) has a higher resolution than potentiometers (T-Flight). Thrustmaster state that it's a factor of 256 but they're quoting over area rather than linear throw so it's really 16x. So you'd imagine that it's like the difference between a high-DPI mouse and a standard one. However, the potentiometers used in joysticks like the T-Flight are already fairly high precision, with around 1,000 divisions over full deflection, so it's more like the difference between a high-DPI mouse and an uber-high-DPI one. In short, the difference in precision out of the box isn't as important as a lot of people think.
Where the T16000M has a clear advantage in precision is in the software that Thrustmaster provide. Custom response curves and deadzones can be set, whereas there's no such ability with the T-Flight. This means that the stick can be set so that it is much easier to make small movements near the stick's centre zone without reducing the response at higher deflections. This makes small corrections, such as those required for precise aiming, much easier than with linear response.
As a side point, it should be noted that hall-effect sensors are contactless, while potentiometers are not. This could have implications for long term reliability, although Thrustmaster's excellent reputation suggests that this is unlikely to be a problem.
Regarding throttles, there is no comparison between using a HOTAS and any other method. Having your hand on a control that is directly mapped to the throttle, coupled with various controls that you can use with the fingers and thumb of that hand, is the best solution by far. Once you've tried it, you'll never go back to a keyboard.