1. No. That process should keep it funtioning efficiently for a long time to come. I'm still using a Paasche H that I bought in 1975, and it stil works great.
2. Buy a pack of pipe cleaners, cut 'em in half, put a few drops of thinner on one end, and run it through the tubing. The best thing you can do is to go to your color cup exclusively. When I first started airbrushing, I used the bottle all the time, but after doing a few kits, I found that I could paint an entire 1/35 tank with my color cup about 2/3 full. I also found I wasn't wasting as much paint doing it this way, either.
3. Not necessarily. Neither of my Paasches (H and VL) have covers for theirs. It's not bad that way...it's the way they were designed. The only thing to be careful of is making sure you hold your brush steady when you use a cup so you don't go dumping paint when you accidentally tilt the brush the wrong way (It took me a couple of times to learn that lesson.)
Hope this helps you.
Gip Winecoff