Are nonclustered indexes used when joining tables? I know that joins of type Sort-Merge don't use nonclustered indexes, because they work by sorting both tables and then joining them.

But I've read recommendations to noncluster index all FKs, I believe that's for helping joining.

Is there then some type of join that uses nonclustered indexes?
Have a look at the query execution plan, that should tell you if it is using an index.

I don't know why a sort join couldn't use an index, keys can be read from the index and then sorted if required, which saves scanning the table.