I don't find anything that specifically describes what you've said, but the "trivial" possibility is described in:

Notification Area Settings. Article ID : 279771

Describes the "default" setting for WinXP: Inactive icons are hidden.
(It may be default, but I've never seen it.)
Right click on a blank space on the toolbar, and select properties.
The "default?" should have a check in the box for "Hide Inactive Icons."
If it's checked, you can click on Advanced Properties, and assuming that the icon is there, but hidden, you're supposed to be able to tell it to "not hide."

Note that this is an old report (2001) and so far as I know I haven't reset anything here, and my "default" installation does NOT have the "Hide Inactive Icons" box checked. The current "default" may have changed, but you still may have gotten a check where you don't want it.

The "general how to" for USB troubles is at General USB troubleshooting in Windows XP. Article ID : 310575

If those don't get things back, there is a possibly applicable hotfix, described at:

You do not receive the "Safe to remove hardware" message when you click the "Safely Remove Hardware" icon in Windows XP Article ID : 883517
Describes a "hotfix" available for some "mal performance" of the Safely Remove Hardware icon. This is a "special" fix that should only be installed if you have the problem described. The icon may have been "mangled" if it didn't work like it should and you went ahead and removed(?) so it's marginally possible this applies to you.
Note: you can only get "hotfixes" like this one from Microsoft Support. (Link in the article). IF the hotfix is what you need, they shouldn't charge for their "support," but they may try to set you up for charges if they think your problem is something else.

A couple of general references describe things that can happen with "improper" disconnect of USB devices, but seem only vaguely related. I don't think they'll fix anything for you, but you might want to consult them as "general interest" items.

For general reference, Windows Explorer seems to stop responding after you remove a secondary hard disk drive Article ID : 833394 describes what may happen if you remove a hard drive while a machine is in "sleep mode." This most often happens with laptops, but the general failure mode – i.e. an open handle – may apply to your case. It has been noted that a USB mouse may not come to life when you "wake up" a computer from sleep mode if the mouse was moved during the "go to sleep" turnoff.

The suggestion in the last article is that you can safely remove a device while the machine is OFF, which might be a workaround method for you.

And an even more general one, at article: …when you try to remove a USB device on a Windows XP-based computer. Article ID : 887740 Note Especially: this article has the link to the "how to troubleshoot USB devices" linked at the top of this post.

John