1. I don't think you need to uninstall it. You may wish to disable it in "until I turn it back on manually" mode so that if multiple restarts occur with subsequent partial download and install cycles you know that your antivirus isn't interfering.
2. No. If something is actually incompatible, or believed to be incompatible [some software vendors have not done the "marking" necessary to identify specific software as Windows 10 compatible] the upgrade will remove it. You often have things removed that are actually Windows 10 compatible because of the factor I just mentioned.
3. It doesn't matter whether you're using Windows Update Assistant or going through the usual Windows Update mechanism for major updates. Software removal, if any, is a function of the update, not the method used to invoke it. I haven't had very many things removed recently.
As an aside, I have no idea exactly how smooth a direct Version 1511 to Version 1703 will be, or even if it will work. You may end up being upgraded to Version 1607 and, once the cumulative update is applied to that, might have to use the assistant again to jump from 1607 to 1703. I have never tried to skip a major upgrade and go straight to the next major upgrade, so what I've said is speculation. Just don't be shocked if it's what happens and please do report back on how things went and whether you went from 1511 straight to 1703 or whether you went from 1511 to 1607. If you do end up on 1607 I would wait for 1703 to occur via the normal Windows Update process rather than forcing it through Windows Update Assistant. You're way past due for 1607, though, so you definitely need to give Windows Update Assistant a shot to see what you get from it.
Brian AKA Bri the Tech Guy (website in my user profile) - Windows 10 Home, 64-Bit, Version 1803, Build 17134
. . . the presumption of innocence, while essential in the legal realm, does not mean the elimination of common sense outside it. The willing suspension of disbelief has its limits, or should.
~ Ruth Marcus, November 10, 2017, in Washington Post article, Bannon is right: It’s no coincidence The Post broke the Moore story