{QaptaHvIS So'wI', Hoch jagh Dujmey DaQotlh}
disable all enemy ships while cloaked

How exactly is the {Hoch jagh Dujmey} to be interpreted ?

(Hoch jagh) Dujmey
the ships of each enemy

or

Hoch (jagh Dujmey)
all the enemy ships

or

Hoch (jagh) Dujmey
all the ships of the enemy
(with the Hoch, referring to the Dujmey instead of jagh)

Is there a way of knowing, which of the three is the correct
interpretation ? Or do we just use the Force to decide ?

It could mean the ships of each enemy or all the enemy ships. The third option is not available, because the Klingon noun-noun construction doesn't let you insert other, unrelated nouns in the middle of the noun-noun. All the ships of the enemy would be jagh Hoch Duj.

Since we're given the English translation all enemy ships, it seems clear which meaning Okrand had in mind. But Hoch jagh Dujmey can be interpreted either way, and the results are not different enough in this context to matter, so no further disambiguation is necessary. Whether you disable the ship of each enemy or all enemy ships, there are no more ships to worry about.

-- 
SuStel
http://trimboli.name