"show procedure status" displaying the non existing databases stored procedures in mysql server
Yes. There is not much else to say about your question. If you have recovered the mysql.proc table, but not the databases, you may see the procedures but not the databases.

This is because you can export and import them logically "--routines", which will create CREATE PROCEDURE statements, or physically, recovering the mysql.proc table. In any case, they are not real physical objects of each schema subdirectory (unlike tables, partitions and triggers).

If they annoy you, you can safely delete them from the table, as they are just rows.