Well I guess I'll throw my 2 cents in....
1) Some installers swear by cleats, some by staples. That's a debate that will go on after we're both gone. Bottom line , It shouldn't make a difference as long as the hardwood is fastened correctly over a solid approved substrate.
2) 4x8 x 3/4 osb over 2x8's, 16" oc ,is an approved substrate.
3) Re: High spots in subfloor where pieced & high spots at seams. The installers need to flatten these areas. I use an edger ( sander). I've heard of installers using belt sanders or similiar disc sanders, whatever approach they feel comfortable with.
4) Re: 3x3 soft spot, & where "sheets don't intersect over the joist". Both areas should be addressed . Depending on the situation and access, either by meens of cutting out, bracing, patching & screwing , or if possible, simply bracing and screwing.
5) Re: Squeeks. Their not going away on their own. Bottom line with a squeek is somethings loose enough to cause the friction of a squeek. Remove loose fasteners, brace, toenail, glue, screw, whatever it takes. Sheeting out with another layer MAY hide some, but they can re-appear.
6) I'm not familiar with Ipe, but I cant think of a reason why the installer feels more comfortable sheeting out with 3/8 ply, under that particular specie
7) Run the Hardwood perpendicular to the joists.
8) Acclimation- I go with a couple weeks minimum on 3/4,under normal living conditions, but nothing's written in stone. Moisture test the subfloor and hardwood,( with a pin type moisture meter), they should be within 2% before installation. Always keep your RH within range.
Sounds to me like you'll know if the installers are doing a good job.