Is there a way to write intelligent queries against a merge table in MySQL that represents a bunch of tables partitioned by date?
When you say merge table, I assume you mean MERGE (Mrg_MyISAM) storage engine.

Without seeing any table definitions, I can easily say this...

The smartest way would be to have each MyISAM table defined with a very good primary key/unique key where the lead column would be the date. At the very least, create an index that uniquely identifies data with only one partition (one underlying MyISAM table).

Each MyISAM table under the Merge definition would have such an index. 

Any other index where the date is not the first column would result in bunches of table scans (NOT PRETTY !!!)

I have two posts I made back in January 2012 on MERGE table usage:


Jan 04, 2012 : get column from too many tables in mysql
Jan 15, 2012 : Separate tables or partition one huge table?


While the Mrg_MyISAM storage engine is still around, most would favor creating a Partitioned Table instead. Notwithstanding, the same rule applies:  create an index that uniquely identifies data with only one partition.