Of course, there should be keyboard/HOTAS assignments for all of the primary functions. I mean, when i fly MSFS on my buddy's PC i never click and drag the throttles,mixture levers, or flaps, i do it with the stick throttle and keyboard.
However, there are lots of systems and functions to model and at some point you run out of keyboard combinations or they become too complicated to remember. That's where clickpits help, because you can keep adding systems without having to worry if the pilot will have enough keys to use them.
For example, the easiest and most often used case is setting the instruments for the course you need to fly. You could do it with the keyboard too, but i just look where the gauge is, pause the TrackIR with a button on the stick to keep the picture steady, place the mouse pointer over the little knob on the gyro compass and roll the mouse wheel...voila, the indicator of the desired heading moves left or right, depending on whether i roll the wheel up or down. Sometimes functions like these provide a faster and more precise control than having to press the same key combination 15 times, like using the trim wheels for example.
The thing is, mouse activated controls should not be primary controls because clicking with the mouse is slower than pressing a key or two (can you imagine having to click the gun trigger on the stick with your mouse? of course not
). However, they are very useful for controls that you don't use all the time and most importantly, things you don't use during combat but are also part of your aircraft, because that means less key combinatios for you to remember. If there's a complex engine start procedure according to real life aircraft manuals for example, there's no reason not to use a mouse. You only need to start the engine at the start of the mission (hopefully), so i guess it's easier to just click through the switches than setup and memorize 4-10 new keyboard assignments
