I'm with Gail, I don't understand what you mean.

Gail earlier suggested that it might be getting your data into cache (not memory buffer, different thing entirely). If the query takes 35 minutes to compile (and that is one seriously long compile time), what does this have to do with data into the cache (which is what I'm assuming you mean by querying the indexes)?

However, if it's about cache, then no, if your nightly processes are clearing the cache (which is pretty common depending on what your nightly processes are doing), then getting the commonly accessed stuff back into cache requires running a query to make that happen.

If this is causing issues, then you need to look to what the nightly processes are and how they're being done in order to see if you can reduce their memory footprint.