Hi. This puzzled me for a moment too, when I first was learning the in's and out's of NT 4.
Here is what I know about this now.
As long as your Server Manager is working properly it should be functioning like this:
The "full colored" iconsunder the normal view mode (that is its set to view ALL computers and the option for viewing just the domain computers is *NOT* checked) will simply show all NT machines (or more accurately NT kernel based) that have a working (aka "not corrupted") computer account and is a member of a valid NT domain.
I'm assuming you already know that the difference between the appearance of the icons represents either a server or a workstation (the "tower case" icon is a server, the other is the workstation).
Depending on the view mode your Server Manager is selected you may see some icons greyed or completely missing all together. In other words, it adapts to your viewing selection.
For instance, when selected to show servers only - the workstation icons will be greyed. When you select the "show domain members only" - the reason you see only a handful of servers "colored in" is because its showing you the PDC's only. So if you have, say, 3 domains on your network and everything is working as it should - you should see 3 server icons "colored in" through server manager - because they are the 3 PDCs of your domains.
What's more is that don't forget that server manager doesn't update "live", it follows the same the guidelines as the browser does. Meaning it updates over a period of time. This is easily proven, simply shut down a domain controller and look at server manager it will still show as a "colored" icon for a few minutes before it updates and changes the status. Likewise, sometimes it'll change status right away - that's because you caught it by luck at that critical update period in the "cycle" of things.