Is there a mandatory difficult base defense at around 18 months of gameplay?

[legionof1]

A kick up the backside to keep the player moving, is not expected to be an entirely enjoyable experience. The way its used here in piratez is pretty well designed. Its neither overly crippling to fail(still expensive) while still being a threat regardless of progression level.   

[Eddie]

Also what's the point of having scout ships, assuming you can intercept the small ships but can't beat a cruiser, so you destoy the first two ships in a crackdown wave, then the cruiser comes anyways and finds your hideout.

Destroying a UFO delays the next one. So by destroying the first two scouts you buy time.
There is no guaranteed chance for any UFO to detect the hideout. Less ships looking for it, less chance of detection.