The bomb is only there if you proceed in the correct sequence. You need to make sure you've talked to all of the five races, following the clues in the correct order before the bomb will show up (ask them all for help). It's tricky since the transporter will malfunction with overuse, and if you foot slog too much the bomb tends to explode before you're done. SPOILER Walk the distances between coordinates when short, only use the transporter for the long distances. After talking to the Thshhath, walk to the wind tunnel and zoom over to the dark side. The bomb is easily visible at the coordinates the Thshhath gives. Disabling the bomb is also a bit frustrating. Just set phasers on stun, Jim!
Note: The 1987 of Kobayashi Alternative is a very different game to the 1985 version. It fixes most of the earlier bugs and has different objectives with an improved storyline. IMO the 1985 version from the abandonware sites should be avoided completely. The 1987 version plays a tune at the intro, and starts your game with engines damaged near Orna. You'll need to visit Orna to repair the engines before you can do much (the 1985 version introduced an end-game bug when visiting Orna). With the 1987 version, don't use the old Apple II walkthroughs you'll find on the net. They're for the old 1985 version which is not the same - just a confused mess.