Without the source code
you'll never know why it did these things. But you can guess:
Encrypted packets were discarded because they were encrypted. You can't read them. To do so would be (a) a waste of computing power and (b) very definitely illegal. Anything to do with wifi should follow exactly the same practice- if you can't understand it you're not the intended recipient. So get rid of it.
Non-encrypted packets weren't discarded because they could pull all of the data they needed from them- I believe this was MAC addresses, mainly. This data was freely broadcast. Anyone could read it- it's analogous to standing on the roof of your house shouting it out in all directions. They didn't decrypt HTTPS sessions- so they don't have your online banking details, work emails, anything copied over a corporate VPN or anything like that.
They didn't hang around- so unless you're really unlucky they haven't got anything that could be used as proof of you downloading movies.
It's not unreasonable to believe that Googles' testing guys tested the tech in their own backyard. And their backyard is in a pretty tech-savvy area. So I'd imagine unencrypted networks would be pretty rare.
And one person wouldn't be able to do this for 3 years. But remember that this is a corporation- layers inside layers. The drivers would just have said the hard drive's getting a bit full and forgotten about it. The tech who changed / emptied the hard drives would have just done his thing and left. It's Google, so they'd not have noticed the relatively small amount of extra data (especially on top of the masses of photographic and positioning data they'd be copying at the same time). Even their MAC-pulling software wouldn't have noticed the extra data. It'd just have pulled the MAC addresses from the captured packets and got on with geolocating them.
It is very, very possible that no-one would have noticed this data was as valuable as it is until it was looked at by someone who actually looked at the data.