Fragmentation typically isn't an issue anymore because Windows will defrag its own drives daily by default. Fragmentation is also irrelevant if you've got an SSD, which I'd hope most people have for their primary drive nowadays. Your registry only grows indefinitely if you're constantly adding new software AND it doesn't clean up after itself properly, something that's a bit less common than it used to now that most programs use the standard Windows Installer libraries.
Microsoft Windows runtime requirements actually haven't increased significantly since Microsoft Vista, which was a *big* jump in hardware requirements (and they significantly understated the minimum requirements as well). MS has actually done a good job at keeping the runtime requirements fairly constant the last few releases, because we haven't seen the constant increase in CPU hardware speed like we used to. If you've got a machine that ran Vista reasonably well, it will probably run Windows 10 as well.
The second issue looks more reasonable to me, as I've seen this happen with terrible AV products and underpowered machines at work before as well. Frankly, the scans should NOT be taking place during the day, as long as people's machines are left on and connected. The whole drive encryption is likely not the issue, as that has much lower overhead than most people expect - it's the security software constantly thrashing the hard drive. If you get two competing programs trying to access the hard drive, access tends to slow down exponentially, because the drive head now has to constantly swap between two different points on the drive to service multiple requests. IT is correct in that SSDs would make a huge difference here, as they don't have this issue.