Using Polyjuice potion is much stealthier
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While SQBs answer is spot on and lists the most important out- and in-universe reasons, there is another aspect: When using Polyjuice potion, the victim may never become aware he or she was spied on. Even if the deception is discovered, this doesn't mean there is any clue leading to the perpetrators (except cui bono and possibly modus operandi, neither really hard evidence).

Veritaserum may be applied secretly, but the victim will still be aware that he or she was asked, by whom, and which questions -- not really the hallmark of successful undercover work.

The Confundus Charm, on the other hand, *can* be used to make the victim spill the beans and then forget the whole affair, but that takes considerably more skill than the simpler applications of the charm. In particular, I deem it difficult to coax reasonable statements out of a confused victim; ["Millenium hand and shrimp!"](https://www.everything2.com/title/Millennium+hand+and+shrimp) is more like what I would expect to hear. Moreover, any failure happens directly in front of the victim -- a sudden end for the stealthy approach. In contrast, Polyjuice potion takes no real skill to use, and the one failure with it (you may remember Catgirl Hermione) happened away from the action and did not impact the success of the surreptitious questioning in any way.