1. Why would I be getting slow speed and a 99% bottleneck at the source when my ESXi is actually my strongest and fastest hardware? Is my backup server not only the proxy but also the source? Would it be struggling that much for only one VM at a time? Then what would be the ESXi server?
This is hard to analyse without looking at your setup. Where is the Backup Server placed? I guess on a separate server to attach the USB3 disk? This would mean that Veeam will run in Network (NBD) mode which is the slowest by design of VMware. Can you install Backup & Replication on a new VM and use a phsical raw device mapping as target (so that you can move it as you whish). That way Veeam would operate in Virtual Infrastructure Backup Mode (HotAdd) which is potentially much faster.
2. Is restoring usually similar, slower or faster than the backup itself? This depends on the setup. I think in you setup the datastore itself is not the bottleneck. So it should be similar.
3. Is doing two Quick Migrations with ISCI faster than a Backup and Restore in Network Mode? If they use the same transport mode, they are nearly equal. It depends on your setup which backup mode they can use. If you work with Virtual Backup & Replication here, it would be potentially faster because of Virtual Appliance mode usage... See my comments above.
4. Is a Quick Migration considered the same server and hardware for the guest? (We have a licenced software that detect even virtual hardware change and could stop working.)
Quick Migration do exactly the same thing as backup and restore. So it depends on your software... Normally the OS do not detect that change. Rule of thumb is, that if you can do vMotion and Storage vMotion with the VM, it should be fine. MAC address change depends on the VMware VM setting. If the MAC address is set to manual, the VM at restore/migration would have the same.
5. I have some vmdk that are on another Datastore that I don't need to move, if I leave them on the same datastore will it still make a copy with Quick Migration or will It skip them? That was not an option with VeeamZIP, it would save some time and I don't think I have enough space to copy them on their current Datastore.
Sorry I don´t know if you can Exclude disks at Backup Free edition. Please try. If you add the VM, you can hit the "Exclude" button and exclude all non needed disks.