Why were the "ghost satellites" such a big issue?

Plot Device.

Now, I believe this statement from the beginning of that Wikipedia article sums up your frustration.

A contrived or arbitrary plot device may annoy or confuse the reader, causing a loss of the suspension of disbelief.

You've got to remember... you are watching a story that someone wrote down... or multiple people had a hand in writing down. It was constructed from beginning to end to take up a certain amount of time, create drama and tension, tell a story and (hopefully) illicit an emotional response or two (or more). If it is well written, you won't see plot issues like this. The story will flow, you will get sucked into it, and at the end you'll come away with a feeling of satisfaction. If it is not well written... well, you get issues like the problem you point out.

There are so many examples of bad plot devices that I can't even begin to provide examples of them. I can honestly say that you can probably rattle off a dozen or more yourself, and you know what I'm talking about. Bad plot devices are extremely common in action movies unfortunately, where the movie itself is written as a vehicle for a specific star (and we are talking about a Steven Segal sequel here) as opposed to a well constructed story that just happens to have well-known actors in it. In general, action movies are not about a good story (don't list examples of where I'm wrong, I know there are good action movies). Action movies are about action. Whatever can be put in the movie to even superficially provide an excuse somewhere for action (or making the star look good) will be put in there.

So you have to ALWAYS bear this in mind. When you spot something like this, you have to resist the urge to ask for the reason why the bad plot device is there. You will rarely, if ever, get a satisfactory answer.

For almost all the duration of the movie, the satellite was under the complete control of Dane's laptop. As such, it would not respond to self-destruct commands, or any other attempts to communicate. It was completely taken over by Dane.

Only when Casey shot and destroyed the laptop at the very end of the movie, the satellite began to respond to communications form the command center, and destroyed itself.

This is simply lame writing. Or probably a collaborative effort by the producer, director, etc., in a small series of steps which transformed an initially decent plot into a lame one.

In WarGames (1983), the computer tries to find the missile launch security code, a 12+ digit number, by using brute force. Somehow it is able to identify when it has a digit correct (lame point #1), so we see it trying the remaining digits in rapid succession, seemingly thousands or more per second. However, after finding all but the last few, it still takes the same amount of time to determine the next digit, when clearly it should take one tenth of the time of the previous digit (lame point #2). That wouldn't be as dramatic, I suppose, from one point of view. Though setting the scene truthfully would bring more suspense, particularly if it were explained how it actually worked.