The advantage to upgrading your ship with fake licenses would be that you don't have to run around completing small quests for NPCs, although I've personally found this much easier than collecting 280,000 pixels. Also, if you buy the first few fake licenses then decide to go the normal route, you'll still have to get up to the number of crew members you'd need normally to unlock the next tier, so your previous licenses have gone to waste. You'll need a total of 280,000 pixels to fully upgrade your ship. These villages can be found on many different planets.

The main disadvantage to upgrading your ship with fake licenses is its cost. In order to recruit crew members for your ship, you first must locate a village. You will not be locked out of side-quests, and can still gain crew members if you want to. Once upgraded, there is no difference between a ship that was upgraded with a fake license and a ship that was upgraded with a real license. Upgrading your ship normally involves getting crew members from NPC settlements (a total of 2, 4, 6, 8, then 10) by completing small randomly generated quests for them, or by hiring penguin mercenaries after defeating Dreadwing.

Starbound getting crew members