We know about them for a few reasons.
A) We can access the game's data. This allows us to see some abilities such as Contrary Serperior or Shadow Tag Chandelure in Gen5 (now Infiltrator).
B) Some Pokemon in Battle _______ have them. For example, an Aurorus with Snow Warning is used in the Battle Facility in Kiloude City.
C) You can hack Pokemon with HAs into games with PowerSaves. Hence, some ugly people have Adaptability Dragalge.