Check the Map/Scene Properties > Extent and Clip layers options. Could be that the points are being hidden by one or both of these settings in Pro. For AGOL, i'm pretty sure you are limited to 2000 points only.
I found a solution using FUSION and PDAL.
First, I used @andre silva's answer from this post to clip my point clouds using the shapefiles so that I created new point clouds for each of my trees and stored them together in a new folder. Clipping LAS data using shapefile polygons and open source software?
The code in FUSION looks like this, where the flag "...