I really think this has more to do with variable interpolation than it does with log4perl.

Comparing example A:

$self->{logger}->trace("total NbObsThis $i=$nbObservedThisNGram->[$i];
+ nbObsAll $i=$nbObservedAllNGrams->[$i]; total=$totalObservedAll; nbE
+xpected $i=$nbExpectedThis[$i]; chisq = $chiSquare[$i]");
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with example B:

$self->{logger}->trace('no interpolation');
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would be useful to demonstrate the difference in overhead between perl internals and log4perl. You're going to be stuck with interpolation performance no matter what logging framework you use.