The error I was getting is described in HSEARCH-1929. I couldn't create an index.

Got you. I linked the two issues.

The workaround I had to implement seems kinda ugly to me: I introduced a transient method which is calling the super class getId method only for the purpose of indexing. getId method is usually introduced in some kind of super class of all entities so it's not cool to add search annotations there.

Hmm, I am not sure I am following.

Meanwhile in 5.2.0.Final which uses the same Lucene version but doesn't have a @Facet annotation my old code works.

Search 5.2 and 5.3 are using the same Lucene version, but the implementation of faceting has changed. 5.2 was based on some custom FieldCache approach whereas 5.3 is using some of Lucene's built-in support for faceting. Partly because FieldCache will be removed in upcoming versions of Lucene and partly because you get a real performance boost using the Lucene provided classes. See also this blog post