Upgrading your hatcheries has many advantages, such as being able to queue more monsters at a time. A level 3 Hatchery, when placed correctly, is able to almost completely hide a cannon, laser, or sniper tower. Unless your opponent knows beforehand that this will happen, it is easily missed. Upgrading your hatchery to level 3 takes 12 hours.
Do not upgrade your Hatchery when you own a Hatchery Control Center, because your Hatchery page is changed to the HCC page, unless you want it to be big to cover up things or having more HP.
To save your Goo from attackers, fill up your Housing with Pokeys, then fill up your Hatcheries with high cost monsters like DAVE or Zafreeti. When the Hatcheries are destroyed, the production is put on hold, but the Goo is not lost.