I am wondering what the new symbol is by the HTML pages in my file manager? It looks like a green skull on a black background.
2nd question. When I deleted a couple of files that were only 96 bytes, I noticed my usage number went down by 4 kb for each file. Is this normal?

It's actually supposed to be
It's actually supposed to be the planet Earth, in as much as an HTML page is a *world* wide web document. Here it is, in greatly enlarged form.

I just now transparent-ized the black background, but I'm not sure it's any improvement.

If you have any suggestions for a better icon, I don't deny it'd be nice.
Second question:
Servers are neat and tidy creatures, and don't just toss files *everywhere*. The hard drive is divided into compartments of 4K apiece. If you have a file of *one* byte, it takes up a minimum of 4K, because as a highly *moral* server, it doesn't allow two files to co-habit one compartment. (The compartments are actually called allocation units.)
A directory is actually a file. Adding a file of *zero* bytes puts an entry into the directory, but doesn't assign any extra storage, so it's sorta free. Except that if you when you add an entry to a directory, sometimes, the directory has to start using 2 compartments instead of one, which means a zero-length file can take up another 4096 bytes of space.
There's been some discussion of webmail clients. Originally, we had three webmail clients on the server - Neomail, Squirrelmail, and Horde - and we stored incoming mail, all in one big file. That's fallen out of favor. These days, you're supposed to use a new format that stores each mail in a separate file, and keeps all those files in a big directory. Neomail does NOT support that new storage system.
In terms of efficiency, the new mail directories make some sense - but every email ends up taking multiples of 4K of disk, instead of its actual size, and even the directories get pretty doggoned big. And if you have a directory with 1000 entries and you delete entries 2 through 999, the directory doesn't automatically shrink to reclaim that space.
So not only do we lose the use of Neomail, we end up wasting a lot of disk space. If it uses fewer CPU cycles, I suppose that's an overall gain - but it sure isn't obvious at first appearance.
Life is a beta...