Warnings can be lexically scoped. Hence:

use strict;
use warnings;

my $str = "junk not junk";

{
    no warnings qw/void/;
    $str !~ s/junk//g;
}
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This silences the "void context" warning but only on operations that occur within the curly brackets. perllexwarn for more fun details.

I prefer this method to your if(){} method, because it is easier to understand if you come along six months down the road and wonder why on earth you wrapped a substitution in an empty if(){} statement. Looking at the no warnings code, you'll remember, "Oh, I'm squelching a void context warning." The if(){} method, you'll look and say to yourself, "What was I thinking?" My way utilizes the primary purpose of the "no warnings" construct. You were well justified in looking for a better way as the method you suggested utilizes a tertiary side-effect of the if(){} statement.

Great question, by the way.