You can still get OTA notifications if you root and do nothing else. Even if you flash a new ROM/Kernel, you can sometimes get OTA notifications.
To prevent OTAs from popping up (and removing SU access) you can do one of many things:
1) Disable the updater. Find and rename updater.apk to updater.apk.bak with a root explorer (es file explorer is a good one and is free). This is found in /system/app directory. If you use ES File Explorer, click the star in the upper right, then select 'Phone'.
2) Disable the updater through System Updates. Push menu button > Settings > System Updates > HTC Software Update > Uncheck Scheduled Check.
3) Change system files. This could be as easy as removing/renaming a system file or carrier installed bloat file (like anything that says sprint). These files are located in /system/app. But, at this point, you might as well just disable updater.apk. Many ROMs make tweaks to system applications, so this is likely already preventing you from getting an OTA (if you flash a custom ROM).