Obtaining root and running on the stock ROM will feel no different than being unrooted. But you will have lots of options/configurations available to you that you didn't have before. None of this will be apparent just using your stock ROM. For example, say you want to scale up the size things show up on the screen? There's a rooted app for that. Or you can tweak config files in the filesystem manually. Find your MSL, wifi tether, over/underclock your processor, etc... there are rooted apps for that. Some of these apps will be in the market; others are available elsewhere.
As for getting updates, this is not as cumbersome as it may seem, and you can thank the huge rooting community for that. Let's say HTC releases an OTA (over-the-air) update. You never want to accept an OTA update if you're rooted. The OTA is designed for a purely stock ROM, and the fact that you're rooted means your phone is one-off from how it left the factory. Therefore, there's no guarantee that OTA functions properly.
So instead, you wait for the rooted version of the OTA update. The process of packaging up such a rooted ROM takes a few minutes for the developer who does it. And s/he does it for the greater good of the rooting community. It will be available within hours of the OTA, and sometimes you'll have access to it before your phone gets the OTA notification.
Flashing the rooted ROM is a very straightforward process, and I will make sure that somewhere in the sticky threads, there will be instructions on how to flash ROMs.
In summary, you can root, and then never take advantage of anything that root access offers, and your phone will work just like it was never rooted. Rooting a phone only offers you more options; it does not change the immediate behavior of the phone. You have total control over how you want to take advantage of root access. You will not be handicapped by having root in terms of getting updates. You just have to flash the rooted update manually, rather than let HTC do it over-the-air for you.
I'd venture to say that once you are rooted, you will discover some neat abilities that you're going to take advantage of, simply because they are so useful (NANDroid backups, Titanium Backup, possibly SetCPU).