Just as in other languages, you can't determine the efficiency of a query based on a character count. Also, 1000 characters isn't what I could call "large", especially when you use good table/column names, aliases that make sense, etc.
If you're not comfortable enough with SQL to be able to "eye ball" the design merits of particular query, run it through a profiler and examine the execution plan. That'll give you a good idea of problems, if any, the code in question will suffer from.
My rule of thumb is this: write the best, tightest, simplest code you can, and optimize where needed - ie, where you see a performance bottleneck or where (as frequently happens) you slap yourself in the head and say "D'OH!" at about three in the morning on vacation.
Summary:Code well, and optimize where needed.
As Robert said, if you can't easily tell what the query is doing, it probably needs to be simplified.