According to Cambridge dictionary, you don't need a hyphen: https://dictionary.cambridge.org/dictionary/english/boxed-in
I did some research about hyphen in the past. There is not an immutable rule that always applies. It's rather subjective and people differ on it.
I guess this would be under the kind of circumstances that prompted the question. The sentence was: Forgive me such a noob question, but in all the videos I've been watching of paludarium set-ups, the design always includes some kind of structure that isolates or boxes-in the pump. Without the hyphen here it could be read as 'boxes in the pump', as in 'the pump contains boxes'.
My first instinct was that boxed-in looks just... wrong. It's boxed in not boxed-in. The hyphen just doesn't fit. For that particular sentence, it still looks wrong. "Boxes in" is a familiar enough phrase (to me, a native English speaker) that I am not gonna read it as 'the pump contains boxes' but 'something is containing the pumps'.
