Thunderbolt is signified by a lightning symbol on the port, if it isn’t there, it isn’t Thunderbolt. That is about the only given in your scenario.
A powered USB-A hub can support more devices, without overdrawing on the supply from the computer. USB-C has higher standards for power draw, so that is less of an issue - unless you are running a laptop off batteries. So, if you have multiple USB-A 2.5" drives hanging off an USB-A hub, at some point some or all will stop working or stop working reliably, because they are exceeding the designed maximum draw of the USB port. USB-C, on the other hand, is designed to power larger devices or to power laptops through the port, so has a much higher theoretical draw - the actual power supply and motherboard tolerances will affect the actual maximum output and a manufacturer who just puts an USB-C port on a standard header designed for USB-A will bring the theory crashing down.
USB-C can be any speed from 2.0 through to 3.2 or 4.0 (not yet ratified and not currently available on any device). Without physically testing, there is no real way to know whether an USB-A 3.1 is faster or slower than an USB-C 3.1 - the controller chip will also make a difference. Is one on the main processor bus and the other on a dedicated chip? Does the dedicated chip have enough PCIe lanes dedicated to it? What else is running over the PCIe line?
Without going down into minute details of the motherboard construction and the chips, you can’t really define which port is faster or slower. For a “normal” mortal, getting the fastest USB device they can and testing each port is the only real way. But for testing modern USB ports, at least those that are “properly” connected and running optimally, you will need a striped SSD array attached to the port, otherwise you won’t be able to reach the theoretical output.
At the end of the day, if all the ports are wired up properly, there shouldn’t be any noticeable difference, unless you are really pushing the USB 3.0, 3.1 or 3.2 maximum throughput through those ports (5gbps, 10 gpbs and 20gbps respectively) and there are hardly any devices around that will push USB 3.1 or 3.2 to its limits - possibly a USB 3.1 or 3.2 10gbps network adapter, but you will need a 10gbps switch and a NAS or server with a good 10gbps port and an SSD array and enough processing power to flood the USB port.