MySQL large databases, unique index effect on efficiency?
For write operations (e.g. INSERT and DELETE) having a composite index will slow things down. However, MySQL can handle tables with MANY more rows than that. If you need to keep the row count to 1k to maintain performance then I would suggest something is very wrong somewhere. Regardless, I would strongly suggest not breaking the data up in this way, you're just giving yourself a maintenance headache further down the line...

What datatypes are the columns that make up the composite index?