Yes it evaluates to true, because undef is zero numerically regardless of where it came from. It also triggers warnings from each side when the undefined value is coerced into a number, which is exactly what the OP was seeing.

freebie:~ 755> cat quux
use warnings;
my $foo = undef;
if( $foo == undef ) { print "true\n" }
freebie:~ 756> perl quux
Use of uninitialized value in numeric eq (==) at quux line 3.
Use of uninitialized value in numeric eq (==) at quux line 3.         
+          
true
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Update: Added something that runs inside the conditional to show that it's not being interpreted as a bareword, both sides trigger the undef-used-as-a-number warning, and that the conditional is true without parens.