To take advantage of Pix4D Cloud when having ground control points (GCPs), I would suggest this article.
There is no limitation regarding the number of images to process on the cloud or on desktop. However, Pix4D cloud can process a dataset of about 1,000 images for an optimal experience with our servers. Please keep in mind that we expect from our users to respect our fair usage policy of the cloud (15 projects/month of 150 images at 15 MP). Based on the fair usage policy and the server capacity, you can for instance process 2 projects of 1,000 images each in a month, plus some side small projects.