While on the server list a player can tell if an admin is on by counting the visible members and subtracting it from the number shown on the server splash page. Could it be fixed?

You can also tell if a player is on by /telling them as well.

Currently it's not possible to do this in the Bukkit API.

As for /tell, I'm looking into it now but I'm fairly certain you can't /tell someone using the vanilla (built-in) /tell.

In my opinion, there should be permissions/commands to do this:
When someone vanishes, they still show on tab, /list, and can be messaged.
Whenever anyone fakequits, they disappear from tab, /list and cannot be messaged.

The way it is currently on the server I play, when I vanish it removes me from tab, llist, and I cannot be messaged. It is annoying, since I am just vanished, I have already fakejoined and everything, but nobody can even contact me.

What plugins do you have? It shouldn't block you from being contacted by /tell. Maybe another plugin is overriding it. When you use /tell, do you see the message you sent?

As for controlling the tab list, that is not currently possible due to bukkit limits.

We have 27 plugins, not gonna list all of them, but a main plugin is essentials.

Apparently Essentials overrides /tell, so it's Essentials doing that. Looking into how to get around that now.

So... apparently there's no way to do that with the essentials hidden system. Either you hide yourself from commands in essentials or you don't, no way around it for admins. So, if you want to /msg, disable the Essentials hook in the VanishNoPacket config.