why is the level of contamination measured as a number of colonies rather than size of colonies?

Answer 1

Each colony came from a single bacterium as it divided. Counting colonies is like counting single bacteria.

Answer 2

The number of colonies is directly related to the concentration of bacteria which is causing the contamination. The size of the colony is not a true representation of the level of contamination as different bacteria form different colony sizes under differing growth conditions, and even the same bacteria can form different colony sizes under differing growth conditions!!