The black eggs are part of a special mission that is explained to you in the game.SHODAN: "[...] before we can separate the Rickenbacker, we must remove the foul black eggs the Many has vomited on this deck. These eggs are an experiment of the Many and will in time spawn the next generation of Annelid, which you will have no hope of destroying. [...]"Actually they never spawn anything, because you destroy them before that happens.