my ($color, $fruit) = (
   $hoa->{keytwo}->[$idx_color],
   $hoa->{keytwo}->[$idx_fruit]
);
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is equivalent to

my $aref = $hoa->{keytwo};
my ($color, $fruit) = (
   ${$aref}[$idx_color],
   ${$aref}[$idx_fruit]
);
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Since you're dealing with one array (@{$aref}), yes, you can use a slice:

my $aref = $hoa->{keytwo};
my ($color, $fruit) = @{$aref}[$idx_color, $idx_fruit];
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or back in one line:

my ($color, $fruit) = @{$hoa->{keytwo}}[$idx_color, $idx_fruit];
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Notice I used <sigil>{$aref}. I did so because it parallels <sigil>array exactly. $aref->[] is a shortcut for ${$aref}[] exclusively, so it's useless when dealing with array slices.

Update: oh, I forgot to answer the second question! There's nothing wrong with HoA in general. In your situation, a hash would work nicely since you're naming your parameters anyway.

If you go with hashes, you can take hash slices:

my ($color, $fruit) = @{$hoa->{keytwo}}{'color', 'fruit'};
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If you go with arrays, why not use constants to speed things up slightly:

sub IDX_COLOR () { 0 }
sub IDX_FRUIT () { 1 }
my ($color, $fruit) = @{$hoa->{keytwo}}[IDX_COLOR, IDX_FRUIT];
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or

use constant IDX_COLOR => 0;
use constant IDX_FRUIT => 1;
my ($color, $fruit) = @{$hoa->{keytwo}}[IDX_COLOR, IDX_FRUIT];
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The combination of the empty prototype and the constant value being returned makes IDX_COLOR and IDX_FRUIT constants rather than functions.