I didn't find any evidence that faceting over multi value fields is deprecated in 5.3.0.Final so it makes me think that it's a bug.

It is not, in fact it is supposed to work only after the recent changes and the introduction of @Facet. There is a test case ManyToOneFacetingTest which shows the use of multi values fields for faceting. The difference here is that the indexed and faceted field is a string. We need to check whether using numeric values causes the behavior you describe. Numeric values are encoded differently, though it might be possible.