A 3km commute can be done on almost any bike but some are more practical than others.
You don't need any suspension on a commuter bike. Cheap suspension is worse than no suspension. As suspension, it isn't very good, it is heavy, sucks energy, needs maintenance and removes the ability to fit standard rack and fenders. In a Gadget Show test of entry-level bikes the winning budget MTB over a course of rolling forrest tracks was a non-sus Decathon Btwin model.
A good quality tyre is much more useful than suspension. Fat tyres can cope with rough roads and puncture protection will ensure that you get to school on time.
18 vs 21 gears is not important on a 3km ride. Generally 21 spd will be higher grade. If you ditch all the suspension and seek out a bike with higher grade components you will be much better off. At entry level, a slight improvement in component grade is a huge improvement in quality.
I have changed cables on several grip-shift style shifters . They are all much harder to maintain then simple thumb shifters.
Rack and mudguards/fenders are best fitted by bolting onto threaded attachment points on the frame or forks . If your bike lacks these eyelets you have to use ugly clamps.