I think they can be helpful for achieving that initial critical mass of understanding around a topic ("a is to b as x is to y... oh okay, I better understand the relationship between a and b"), but yeah, if you don't unwind the analogy afterward, then it can be a false understanding.

I found this kind of thing a struggle in engineering math courses, where you'd often move equations into transformed spaces (frequency domain, whatever), perform operations on them, and then un-transform them to pop out a result. It's like, yes, the transform is obviously an immensely powerful abstraction, but I didn't really trust what was going on in there unless I did at least a few of the exercises from first principles as well, in order to prove to myself that doing operations in the transformed space was "safe".