Multiple accounts on SO are merged if they share the same IP/OpenID/etc. However, is there a way to analyze upvotes statistics to detect "cross-pollination" of some accounts which regularly upvote each other? I.e. some new user spends most of the upvotes upvoting the answers of the other for some long period of time. Is there a tool do detect it?
Multiple accounts are not necessarily merged, and certainly not automatically. You are allowed to have multiple accounts as long as you do so responsibly and follow some basic ground rules.
Moderators will only manually merge user accounts if there is evidence that they are violating those ground rules, for example conspiring to commit vote fraud.
So yes, these "cross-pollenation" tools that you describe do exist, but they are only available to ♦ moderators because they are based on statistical information about voting and other patterns that we don't want to fall into the wrong hands.
And not all of them even require moderator intervention. For example, there is a process that runs every 24 hours to detect and automatically reverse instances of vote fraud.