Choosing between imperfetto and passato remoto/passato prossimo is sometimes difficult for people speaking languages where this distinction is missing.
English has a kind of imperfetto with the construction used to or the progressive form, but they don't fully overlap.
I used to live in Rome when I was a student ↔ Abitavo a Roma quando studiavo
I was living in Rome when I met my girlfriend ↔ Abitavo a Roma quando ho conosciuto la mia ragazza
Once I was a boy ↔ Un tempo ero un bambino
Both Italian sentences have the imperfetto. In the third sentence there cannot be the passato (either remoto or prossimo), because we need to convey the idea that being a boy lasted for a period of time.
Different languages, different use of verbs.
In your sentence, the ships existed for a period of time, during which they transported supplies, so you have to use the imperfetto:
Al tempo c'era una quantità di navi che trasportavano rifornimenti
I wouldn't translate “number” with numero, in this case, because it denotes an undetermined quantity. It could also be un certo numero. Yes, to express an undetermined number we use certo, but such usage is also common in English for “certain”. Even better (thanks to DaG)
Al tempo c’erano numerose navi che trasportavano rifornimenti.
The problem whether the verb trasportavano is conjugated with the grammatical subject (quantità, singular) or with the logical subject (navi, plural) has been discussed on the site, for instance at Is 'c'è' or 'ci sono' used with "un sacco di"