Is there a difference between "Thunderbolt" and "Mini DisplayPort" cables?

Yes, they are different. Display Port is a passive audio/video technology, Thunderbolt is active generic data technology. The hardware inside the cable is necessary to get the full data throughput. A Display Port cable will only carry Video/Audio to an attached monitors^*, while a Thunderbolt cable is able to carry all sorts of other data, which is required for your dock with multiple types of ports.

Whilst you can get away with connecting one monitor to Thunderbolt with a mini-DP cable, that's the end of the chain.

In order to chain, you must have Thunderbolt cabling throughout.

See The technology inside Apple’s $50 Thunderbolt cable

Thunderbolt carries Displayport 1.1a video, and will not work with some newer monitors, including 4k monitors. One will need at least DP 1.2 spec cables to power 4k monitors.

Thunderbolt also carries data - 4 high-speed PCI-E channels - in addition to DP 1.1a.

^*: Or to multiple monitors is all devices support DP 1.2 with MST.

Difference #1 - performance. The comparison chart below illustrates just how efficient Thunderbolt is with handling media files:

Difference #2 - compatibility. The image below shows which combinations of Thunderbolt (TB Cable) and Mini DisplayPort (DP Cable) will work (marked green) and will not work (marked red) together: (click to see large picture)

Read more in StarTech blog.

According to this source and also this source, you will not be able to use a Mini Display Port cables instead of Thunderbolt cables.

MBA = Mac Book Air.

Mini DisplayPort Cable

       OUT       |        IN        
------------------------------------
Mini DisplayPort | Mini DisplayPort
Thunderbolt      | Mini DisplayPort

Thunderbolt Cable

       OUT       |        IN        
------------------------------------
Thunderbolt      | Thunderbolt

Nothing works for Mini DisplayPort to Thunderbolt.