I don't know if this has been answered already but this has been my experience. First off, you should not need to say TOP 1000 because the custom query editor will ask you how many rows do you want to limit the resource too. Second, I have not gotten * to work, so you need to individually declare each column. This is good practice anyways.
So, to get the query listed at the begining of this thread, you just need to add the WHERE clause like you did. Here is the same SWQL query with the WHERE clause. Note that I added AS to the tables to make the syntax shorter overall.
SELECT a.TriggerTimeStamp, a.ObjectName, b.ObjectType
FROM Orion.AlertStatus AS a
JOIN Orion.AlertDefinitions AS b
ON a.AlertDefID = b.AlertDefID
WHERE b.ObjectType='Node'
