When the game was newer, the Metaverse was apparently a way to have competition among players in a game w/o multiplayer. High scores, total Empire scores, etc were a source of interest. Many players had discovered tricks or even exploits and tried to keep them "secret" within their Empires. See the "Economic Powerhouse" post by Mumblefratz for one such example.
One I discovered independently involves a simple way to get a slightly better planetary starting setup. I sometimes still use it, but only on Suicidal.
The spy bug you referenced has long been known. The player who first documented it noted that when a race was exterminated with spies assigned to it, that the spies did not really die, but simply could never again be accessed. For example, the intel level on the extinct race will continue to increase and the player will even get notifications when each increase occurs, though the race is gone! The player described it as the spies "becoming archaeologists."
Spies placed directly on improvements on specific planets do appear to have effects. That is, they appear to deprive that planet or empire of the benefit of the improvement while they are there. I say "apparently" because i have never been able to prove it. In some cases, they seem not to have an effect. Very rarely, a player will get notified that a tech has been stolen by espionage from a race that has at least one spy assigned to a planetary improvement. There reportedly is no relationship between which improvement is targeted and the tech that is stolen.