Changing the target of the wave is more deadly than having the wave hit the normal target. And at high difficulties, the warning is around 1:40. So by the time you get the warning, you need defenses in place already or you won't get there in time. It is actually more dangerous to lower difficulties were a player doesn't normally need as solid a defense. Which would be why there is a cut-off based on difficulty. Because no one needs to see those at Difficulty 5. And again, it could be 1/2 warning, or something. Try playing with No Wave Warnings for a bit. You'll find it isn't as challenging as you thought. It gets old pretty quickly in my opinion, which is why this would happen only once every 8 hours or so.
@Minotaar:
Unannounced Waves are far less punishing than Beachheads, and much more rare. On the invisible upgrades front, these are single, large, unique units that have a visible indicator on their icon. These are units players are already paying attention to. They would be rare enough you could get an alert when one is present in a wave (or attacking your systems in general). Adding more Guardian types is good, but adding 16 Champion types multiplies the existing Guardians by 16 in terms of creating diversity. You get a ton of additional content for some one-time setup of the internal Champion code. Then as more Guardians or Champions get added, the number of combinations grows. At the same time, since each piece (the ship type and Champion type) is separate and understandable, the player is very easily able to identify the capabilities of each dynamic Champion.
For reference, there are 20 Guardians. With 16 Champion types, you get 320 possible Champion Guardians. There isn't even a chance 20 new Guardian types will get added anytime soon, much less 300.