>If the Mojo 2 does not have a proper line-out and it connects to an amp through the headphone-out, isn't it basically double amping?

The Mojo 2 would be fine to use with the A90 Discrete, provided that its output voltage doesn't exceed 2.9 Vrms (high gain input sensitivity).

>Would I gain anything by adding an amp like the Topping A90D?

No, just a lighter wallet. If you wish to alter/improve the sound of your headphones, try experimenting with EQ.