Then a Juggernaut 2 comes along and utterly destroys my fleet of Mark 3s and lesser ships, and eats a colony. It had 400 hit points, so my fleet only slightly scratched it. If it happens to move to the right stars it could easily destroy my entire empire in the next dozen turns.
There are a couple of things you can do about that:
1) Research Laser. I usually arm robotic hulls with Lasers in the early game, so three or four of them can reliably take out a Juggernaut, particularly when defending a system, since there are other things for it to shoot at.
2) Research some stealth techs. Juggernauts aren't very bright, so even a species with no stealth bonus should be able to hide from it by researching Absorption Field (Damper Field should hide you from Small Juggernauts, and Dimensional Cloak should hide you from Large Juggernauts; you'll probably want Phasing Cloak before the Black Krakens show up). Death Spore and Bioterminator only work if the monster's detection is higher than your stealth - also, monsters won't stay around your planets if they can't see them.
Those new structure values for monsters seem rather excessive.
I would hope so. If anyone can win on their very first playtest, I'd say I've failed in making the game adequately challenging. For reference, I'm on my fifth playtest, and I think I'm on the verge of actually winning for the first time.
Also consider that the player can capture nests producing these things-- a single one should not be so invincible.
That's true. A good strategy is to capture monster nests and find a strategic defending location to place them that also meets their location requirements for upgrading to a better type of monster. In the long run, I expect that when there are competent imperial opponents, it will be reasonable to make them weaker, but since their sole purpose right now is to provide a challenge, worrying about the player having an excessive advantage over other empires due to having a monster nest isn't yet relevant.
Also i didn't see any sit rep message when the Juggernaut ate my colony.
In the very recent past you would get a sitrep message saying "The entire population of XYZ was lost to famine!", but I suppose that doesn't happen anymore. I should probably add a sitrep message effects group to the death spore/bioterminator ship parts.
Edit: Also, I agree that the monsters now are probably a bit too powerful, but more due to the terrifying monsters that the Experimentors send out, rather than the natural monsters that show up.