Yeah. If the 10 second or less (MUCH less CD later on) bomb gets cleansed, then you as Zil have done a PERFECT job of harassing. Ta da! After 2 seconds your teammate(s) can jump in and obliterate them because they blew a cleanse on a low damage harassment spell instead of on a stack of CCs.
If people in your games are using cleanse on this ability, then that makes Zilean one of the best cleanse counters in those games, wouldn't you say?
If your opponent is using cleanse on your bombs, you'll know. If you know, tell a teammate to come and set up. Once you do that, rack 'em up and knock 'em down! Your minor loss in damage is now a huge advantage.
Can they cleanse it early game and hurt your mana supply? Sure. Nab a sapphire or something. Can they do it for very long without getting themselves into major pickles? Doubtful.