Yes, a countertop reverse osmosis system will still waste water. In this case, the wasted water will collect in a wastewater compartment. When this compartment is full, the system will alert you, and you'll need to remove it and empty the water before the RO process will continue.
Countertop RO systems don't waste any more or less water than under-sink units. The exact amount of water wasted depends on the brand you buy from.