You'd have to cite some section of the rules where that phrase is applied to spells. Context matters.
Take the spell "Stone Fist" as just one example. "While this spell is in effect, your unarmed strikes do not provoke attacks of opportunity and deal 1d6 points of lethal bludgeoning damage (1d4 if you are Small)."
So, once again: how exactly are you defining the phrase "in effect", in such a way that it makes sense that both spells and performances can be "in effect", since they clearly both can be (and have been) described using that same term?
Finally, the last sentence says that only one bardic performance can be "in effect" at a time. Given that the other rules in this paragraph have all been talking about 'per round' performances, in context I take this one to be so also... you cannot 'maintain' two performances simultaneously. However, that is then no bar against completing one performance which has an effect that does not need to be maintained and starting another.
Specific trumps general. Sure, Deadly Performance gives specific exceptions to the general rules for bardic performance. That doesn't mean that other sentences in the same paragraph also don't apply to it, unless Deadly Performance also calls out a specific exception for those rules. Same with Triple Time.
If the rule had been that the Bard can't maintain two performances at once, then the rule should have talked about the act of maintaining rather than whether the performance was "in effect" or not.
Because, as seen in the case of the Stone Fist spell, you do not need to be actively "maintaining" something for that thing to be considered "in effect". They're two entirely separate concepts.