Odd that none of the top ten sites running vBulletin have these issues. Odd that vBulletin dot org doesn't have these issues. It's a myth. But I DO recommend the latest version of vB 3 and always have. I sort of confused where you were getting from that article, that people shouldn't upgrade to version 3's highest tier. Of course they should, but no further IMO.
This sounds more like having to do with your host, not your software.
I DO recommend upgrading to version 3.8.7 however, but no "higher" until 3.8.8 is released.
Large sites, and sites like vBulletin.org likely have staff capable of fixing security holes themselves and do not require patches from vBulletin. Obviously if you have a capable PHP/vBulletin coder on staff and can fix your own security exploits it's not as critical- but for most- it is.
3.8.8 Beta is as stable as any other version. I myself will be upgrading to 3.8.8 Beta once Beta 3 is released. It's time.