Hi sasmimo,
I understand that you have some questions about using a Thunderbolt Display and multiple external hard drives in a Thunderbolt chain. I know it's nice to be able to easily connect all of your devices, so I'm happy to clarify this further for you.
For the configuration that you've described, which is from a MacBook Air to a Thunderbolt Display to two external hard drives, you should have no problem. While multiple devices on a chain may impact performance, this few devices should present no noticeable problems. You can read more about using Thunderbolt in this way here:
OS X El Capitan: About Thunderbolt
About connecting multiple Thunderbolt devices
You can connect multiple Thunderbolt devices to each other, then connect the chain of devices to the Thunderbolt port
on your Mac.
Only the device directly connected to your Mac receives power from the computer’s Thunderbolt port. The other devices in the chain must be powered by separate power adapters.
A DisplayPort device must be the last device in a chain of connected Thunderbolt devices. For example, if you want to connect both a Thunderbolt hard disk and a DisplayPort display to your Mac, connect the display to the hard disk and then connect the hard disk to your Mac.
Apple Thunderbolt Adapters: Frequently asked questions (FAQ) - Apple Support
Are there other requirements for using these adapters?
If you are connecting multiple devices ("daisy chaining"), at least one computer on the Thunderbolt chain needs to act as a host.
Can other devices on the Thunderbolt chain affect the performance of these adapters?
Yes. Mass storage and other high-bandwidth devices can affect the performance of these adapters. If you have issues mixing the Thunderbolt adapters with such devices, connect devices directly to another Thunderbolt port on your computer, or connect them to low-bandwidth devices on the Thunderbolt chain.
As for the external hard drives, they are mounted in OS X in the same way as a USB hard drive would be, so it is best to eject them as you would normally.
Thanks for using the Apple Support Communities, cheers!