No....it will still be modded. The only change is the version...if you deleted bloatware with root tools or manually, you'll just do that. Wipe cache before or after install so your apps will respond nicely to the update. Some may force close otherwise
Ok I have never done that or had to do that, but in Jrummy's DX/D2 Overclock app there is an option to "clear all data & SD Card cache" ... is that what you mean?
I just want to avoid any hassles, I've read alot about OTA updates removing root, and I, being a noob at rooting, made darn sure I did it right the first time, I was scared to death of bricking my new Droid LOL