Interesting. Either there is a bug in pgAdmin, or you're connecting to a different database that is missing the primary key. What is the EXPLAIN ANALYZE output if you execute the query you sent on a psql prompt?
"alf_node_pkey" PRIMARY KEY, btree (id) CLUSTER would indicate to me that there is a PK on alf_node table, it is on column "id", it is of type btree, and the table is clustered around that index.
Am I reading this totally wrong?
No, that's right. But that wasn't in the SQL you sent. In fact, there's a lot of stuff missing in that output.
Try running the EXPLAIN ANALYZE using the same psql connection you used to retrieve the actual table structure just now. I suspect you've accidentally connected to the wrong database. If it's still doing the sequence scan, we'll have to dig deeper.
I see "CONSTRAINT alf_node_pkey PRIMARY KEY (id)" for table1 and "CONSTRAINT alf_node_properties_pkey PRIMARY KEY (node_id, qname_id, list_index, locale_id)" for table2. When you say there is not primary key defined, is it based on the execution plan ?