One of the first things you learn when you’re rooting is that you never take an OTA update. OTAs will always patch security holes that you used to achieve S-OFF, or they’ll ruin your root access, or they’ll generally cause a bunch of headaches.
If I’m not mistaken, every previous HBOOT update that came with the HTC EVO 3D, or the original EVO 4G, or the EVO 4G LTE, has broken S-OFF exploit methods. So when Sprint finally released ICS for the HTC EVO 3D, there was no reason to suspect that would not be the case again.
If you’re rooted and unlocked, chances are you’ve been on ICS for quite a while now and this doesn’t apply to you. If you’re not in the root game yet and realizing now that this is most likely the last major operating system upgrade the EVO 3D is going to get from Sprint, you’ll still be able to fully enter the root world at a later date with HBOOT 1.58.
Basically, if you’ve been on the fence about taking the update, you should be good for rooting later.