There's any clue on why Battle Programmer Shirase ended so abruptly? I couldn't find any interview or related material about it, even in Japanese. It's sad that is, 14 years already? Without end or an explanation.
As most tv shorts, it ended prematurely, and there's is no secret about it. Most tv shorts ends like that.
You probably got confused because there is only "5 episodes". But in fact, 15 episodes were broadcasted at that time (3 episodes per arc, resulting 5 arcs in total).