1. They did notice, that's how the foundation found out about them and got them all into containment. Could probably have done something with that but meh.
2. I'd say it's based on calculations of how quickly the reproduce and how long they've been in containment. The foundation doesn't have an exact number, but they can approximate it. It's also why after the incident they decided to restrict populations to 500,000, as that would give a significant amount of leeway before things got bad. As for why they started doing that at 1,000,000, I have no idea. Anomalous shenanigans or hive mind smarts or something.
3. Oh you know, guns that shoot spiders, whips made of a bunch of spiders strung together, whips made of spiders covered in guns that shoot spiders, silkswords, missile that explode into spiders, giant spiderlaser cannons, etc. Maybe even smaller spiderbots. Just all the spider weapons. All of them.
