Comics Genesis didn't always save every site- I can think of a handful of those "lost" comics were originally, if not CG, then KeenSpace.
And as noted earlier, KeenSpot/ComicsGenesis appears to be somewhat on it's way out, too. If you go to KeenSpot's home page, they list just 17 strips as "currently updating". And if you actually check those, even a fair number of those aren't updating with much regularity.
"God Child" hasn't updated since May of last year, "Marry Me" has only added one page so far this year, "Yirmumah's" only update since 2012 is a post saying he's moved to Facebook, "Sore Thumbs" hasn't updated in 14 months, "Rumble Fall" hasn't updated since 2014, the author of "Out There" basically quit in March of last year, and "Head Trip" hasn't updated since a month before that.
Which leaves just ten- nine, now, as one of those remaining ten was "Gene Catlow".
And out of those ten, the only one I actually read with any regularity is "Two Kinds". I've never even heard of most of the rest, and at least three of them seem to be nothing more than "comic book teasers"- the first story of a print comic book or graphic novel posted online to get the readers in and interest up, but you have to buy the print books to read more.
Comics Genesis hasn't allowed "domain parking" since 2009, and so in their list of over a hundred comics, the majority of them have been closed and deleted.
On a similar note, I recall a rash of disappearances all within the space of about a year or two, about the same time "Mac Hall" ended- over a decade ago. And the reason was similar to Mac Hall- the authors had been doing the comics while at college, and were hosting them on college servers.
Once they graduated, if they weren't careful, they shortly thereafter lost access to their accounts, which were subsequently deleted.
I recall reading about one author specifically- I can't remember the comic itself, but I remember I was a regular reader, and wondered why it suddenly disappeared one day. She posted on a comic board- possibly one of the old Halfpixel boards- that the comic was gone gone. Her laptop had crashed with a full data loss, and she didn't know the university cancelled accounts of graduates something like 30 days after graduation. Once it was deleted, all her strips disappeared with it.
Another, around the same time, had registered their domain using their college .edu email account. He never got his renewal notice, and one day the site got suspended. All the contact info was stored in the .edu account, which he'd stopped using quite a while before, and had long since been deleted.
Essentially he got locked out of his own site, which was then suspended, then deleted, again with a loss of most of his strips.
You know, I wish I'd been writing a bunch of this down at the time- a "history of the webcomic" would make a pretty interesting book.
But really, there's also a fair number of authors that don't want their stuff online. Plenty of them are going to look at their early works with some revulsion, and a lot of them went on to become professional illustrators or graphic artists- and thus might not necessarily want that old, crummy art hanging around the internet with their name on it. I know Ursula Vernon pulled some of her early stuff for that very reason.
Going along with that, I know of one comic whose author wrote some of her early stuff as a kind of therapy- she had some emotional issues that she said putting down on paper helped sort out. Another did a webcomic detailing his wife's battle with, and finally loss to, cancer. I can see authors like that not necessarily wanting those works online anymore, either.