1) That is a good idea. If you so choose, you can take Negative Qualities reflecting cyberpsychosis or something like that, but it isn't a requirement.
2) You don't get the essence back, what happens is you get a "hole" that you can later fill. EX, if you rip out a Cyberarm and put in a Deltaware Cyberarm, you would still have .05 essence, but 5.45 essence of ware (rather than 5.95). If you then put in, say, a second Deltaware Cyberarm, you now have 5.95 essence of ware and .05 essence, so you don't lose more essence.
Basically, your essence is 6 minus the most 'ware you've ever had at one time.
There's one expensive treatment thing that boosts it up to 6 minus your current ware.