Should I store my cr2 files in the aperture library?

I have noticed aperture slowing, pausing and even crashing recently. I was wondering if storing too many cr2 files in the aperture library might cause this. At this time I have a little over 6000 cr2 files in the aperture library.

Generally, no.  And generally, size alone is not a problem.
I regularly run Libraries with 30,000 24 MPxl Images, both from the system drive or from external drives, and have no problems.
I built up a Library of 1 MB JPG Images to 300,000 Images in order to test Aperture and did not encounter any problems except with Faces.
Although I haven't tested it directly, my sense is that Aperture performs better with large Libraries when the Images' Masters are Referenced and located on a separate drive from the Library.  Put the Library on your highest-performing drive (almost always the system drive); put your Referenced Masters on a fast drive.
The first things to check if Aperture begins to behave poorly are (off the top of my head):
- drive space (Aperture needs a lot of free space on your system drive
- other programs (Aperture is hardware intensive; a poorly written utility can slow the OS a little -- but that little can hobble Aperture on that machine)
- Library corruption (Force-quitting can do this -- run "Repair")
- File fragmentation (OS X does a good job preventing this, but I still recommend defragmenting large Libraries once a month.  Copying to a second drive, and then copying the copy back, defragments files.)
- Also, make sure your copy of Aperture is up-to-date.

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