Yes, unless you get back to 100% stock "out of the box as purchased system software" the new update will not install at all or correctly...this will be the same with the next update...if you don't have this new 2.2 OTA installed in virgin unmolested form at the time that update is released ...then you wil not be able to install that one either...and so on and so on....UNLESS or until some smart person breaks the bootloader.
Sure, you can get the "system leaks" that are available, but as I said those are only part or less than half of the update, and sometimes not the most important part.
Concerning "issues" with the update...the only real thing that can cause such issues is because it was attempted on a non-original "molested" system area... If there is a problem otherwise related to the 2.2 update on a pure stock system, all it takes is a call to VZ and a replacement phone will be on the way to you.
Besides that, by not updating you are missing out on a lot of new features and performance enhancments....it makes no sense at all to me to even consider for a second to not update..but that's just me.
In almost a year of working with Droids, I have never met an Offficial Update I didn't like better than what I had before
