You answered some of my questions, i.e., you are working with file geodatabases on local storage.
Have you had a chance to re-run the query without closing out your connection to see how much of your run time may be related to overhead in creating the connection itself.
In terms of comparing sizes of data sets, size on disk is only one aspect. One needs to look at numbers of records, numbers of fields, types of fields, etc.... For a query where you are only looking at a specific field, the number of records could be a bigger factor than overall size of the data set.
Also, have you tried modifying your query to not select all fields, e.g., "SELECT count(OBJECTID) FROM blk WHERE OBJECTID=1 or OBJECTID=2".