I would like to make a slideshow using 6,000 different square png images with white backgrounds -- race through them in :30 - :45. In theory, is this even possible due to the size? Am I correct in thinking I would have to reduce the size of the images so much they would end up too pixelated? I would follow Andrew Kramer's slideshow tutorial, but I don't want to start this if I will end up with a massive unusable file. Thank you.
There's one key question for which we need an answer: WHAT ARE YOU SUPPOSED TO DELIVER?
What's the playback device? What kind of file does it require for playback? What are the horizontal & vertical dimensions it plays?
Answer that question, and it will go far in guiding what you do in AE.
MP4 video to play on web site. Each image is square, can be any size needed.
Good. In that case go with either 1920x1080 @ 29.97 fps or 1280x720 @ 59.94 fps. Square Pixel. The reason -- it easily can be re-purposed in the future if need be.
AE shouldn't have any problems with the image sizes, nor should it have any problems scaling down. Scaling UP is a different story. Just pick a scale that looks good & have at it.