First of all, you should not have an unbounded array field in your document - this will be a bad design and will lead to problems later on. There can be an array field with large number of bounded elements. You can define index on an array field - these are called as Multikey Indexes.
I suggest, you create some samples of data in your collections and try some queries - including the $lookup queries. Use the explain with “executionStats” mode and study the query plans.