Small (nano) satellites and cubesats are between \$100k and \$500k. What percentage of the total is the cost of the propulsion system?
This is an extremely difficult question to answer, firstly CubeSats and Nanosatellites can cost upwards of 5-10 million depending on the mission type, hardware, and organization developing the spacecraft.
Getting into propulsion systems, this is again a very difficult question to answer accuracy, mainly because of the different types of propulsion systems available widely vary in cost. Cold gas systems for rcs are relatively cheap on the order of around 10-15k per thruster, while chemical thrusters can range between 20-500k+ it largely depends on the technology. Moving into electric things get even more tricky, as EP (Electric Propulsion) systems usually cost more then traditional chemical (mono/biprop).
However, in general cold gas thrusters are usually the cheapest, chemical (mono/biprop) are in the middle, and electric are usually the most expensive. In terms of what percent of the spacecraft it is, largely depends on the mission type and size of the spacecraft (CubeSat, 3U vs 12U).