Hm, same here, although it's bash that's hanging waiting for input, not Perl or the backticks, as in the OP.

$ perl -wMstrict
print qx|printf "%b" "this is a q\'uot\'ed test"|, "\n";
print qx|printf "%b" "this is a q\'uot\'ed test|;
print qx|printf "%b" "this is a q\'uot'ed test|;
__END__
this is a q'uot'ed test
sh: Syntax error: Unterminated quoted string
sh: Syntax error: Unterminated quoted string
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