I have Malachite crop with 20/31/10 stats, and when harvested by Crop Harvester it results in 1-2 copper dust dropped. When harvesting by hand it yields 15-16 dust.
Version is IC2Classic+1.12-1.5.5.
Is it an intended behaviour?

Yes, auto-harvesting is massively weaker than manual. Very intended.

Yep. Very intended.

To give some lore:
The player carefully picks the crop drops while the machine just mashes down the crop and gets as much as it can.
Since the machine is very crude there is a LOT of waste.