Hi Komet,
The limit for ImageIntegration working with FITS files is 8192 images on FreeBSD, Linux and Mac OS X. On Windows, the limit is 4096 images. For the rest of processes, including StarAlignment, there is no specific limit.
Of course, the actual limit is always imposed by the size of your RAM. ImageIntegration works by integrating strips of pixel rows. The number of rows per strip depends on the Buffer size parameter (the default value is 16 MB). By reducing Buffer size you can integrate more images, at the cost of less efficiency. If you set Buffer size = 0, then ImageIntegration will work by single rows, which is extremely inefficient (basically that prevents parallel processing completely) but allows you to integrate the maximum number of images possible with your available RAM.