OK, from the software build number you quoted I think you've got a Sprint model (I Googled "HTC M9 3.41.651.4" and all of the results refer to the Sprint M9). Sprint is a US carrier, and moreover is one that uses a technology called "CDMA", which is used only by a couple of North American carriers and almost nobody else. That means that your phone's hardware will be different from a UK model and you can only use software that was written for that model.
Your phone has been "rooted" by a previous owner, i.e. hacked to enable you to run user apps with system privileges. SuperSU is an app that is used to control root access. By the look of those messages the app has been updated, and now wants to update the superuser module that's been added to the system. Unfortunately the previous owner was an idiot: rather than root the sensible way, installing a custom recovery and using that to root, they've used some dirty hack (or else replaced the custom recovery with the stock one), because you only have the standard recovery module on your phone. This means that it will not be able to update the superuser binary. It's possible that some of your other problems are due to the way the previous owner attempted to root, but I haven't enough information to say.
You'll never receive updates over the air for this phone, as you'd need to be using it with a Sprint contract for that. Also it's not a good idea to accept over the air updates on a rooted phone anyway (can cause problems).
So, what are your options? I'm a little nervous here because I don't know the history of this device and it's a model I've no personal experience with (a Sprint handset), but with those caveats:
* Return to stock:
You should be able to return it completely to stock and update the software in the process by using the download and instructions at
http://www.htc.com/us/support/htc-one-m9-sprint/news/. This will remove the modifications that have been made (completely overwrite them). It
shouldn't lock the phone to Sprint SIMs again, but since I don't know whether it was unlocked officially or via some other method I cannot 100% guarantee that. It will factory reset the phone in the process, so back everything that's important up before trying this.
* Root it properly:
i.e. install a custom recovery, allowing you to replace the hacked ROM with a better custom software. If your bootloader is unlocked (it will say either "locked" or "unlocked" at the top - this is different from SIM locking by the way) you can easily install a custom recovery and then choose a ROM. If not then unlocking the bootloader will also factory reset the device, so again, backup. If you want to investigate this route let us know: I can post more information but as I have a work appointment in 5 minutes I don't have time now (and will be offline for many hours after I press "post" here).