I have deleted the apps in the hope of getting more space, plus I wanted to get rid of the useless icons (it did work for Wii U Chat for example, but it did not for Miiverse).No, I did not delete the chat or safety apps (or any NAND apps actually), frankly I'm shocked you did and that everything works as well as it does. I would have been scared that deleting such NAND apps could brick my Wii U. The only NAND change I have is my custom wara wara plaza, which was no issue for the update and stayed as the custom one i installed.
Anyway, this sounds like your issue in updating to the new firmware. You really don't need it though, it adds nothing (at this time anyway, I see that is theorized this update will maintain Wii U online experiences after Nintendo changes their servers). But maybe if you could get those apps back on your nand via ftpiiu you could then update? But I'd be wary of that potentially bricking too. Probably best to just follow the tutorial to remove the update notification if you haven't already.
Also, my Wii U has been a bit unstable even without touching the NAND, I was happy when they annonced the 5.5.5 one since it would help with stability and potentially fix my problems, but bam, the console refuses to update :/
And I can't play online if I don't update (although I can use NNU-Patcher, but it's annoying having to set it up everytime I need to go online)
I will probably set up RedNAND and start tinkering there in order to "debug" the problem via trial and error, that's what I did for the system apps in order to be sure that they are safe to delete, I have multiple NAND backups before I started touching my Wii U anyway, so I will be able to see what I modified.
Still annoying that nobody bothered in developing something like a boot2 solution to restore the NAND backup without the need to solder... Yet we are getting useless ports of games like Mario 64 (C'mon, that one is even on the VC) and GTA 3 (that any potato PC can run...) Oh well...