Looks like this can be done with mtools. Writing a wrapper for mtools shouldn't be too difficult. I'm surprised that nobody has done this before.

Linux does have a native way to access FAT attributes of a mounted FAT filesystem, it's just not easy to find documentation about it. The interface is an ioctl.

First, let's import some constants from a linux header file (you could just hardcode the numbers but this is more elegant).

Create FatConst.xs with the following contents. (By the way, does someone know if I'm supposed to use ExtUtils::Constant?)

#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"

MODULE = FatConst  PACKAGE = FatConst

#include "linux/msdos_fs.h"

I32
ATTR_RO()
    CODE:
        RETVAL = ATTR_RO;
    OUTPUT:
        RETVAL
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int
FAT_IOCTL_GET_ATTRIBUTES()
    CODE:
        RETVAL = FAT_IOCTL_GET_ATTRIBUTES;
    OUTPUT:
        RETVAL

int
FAT_IOCTL_SET_ATTRIBUTES()
    CODE:
        RETVAL = FAT_IOCTL_SET_ATTRIBUTES;
    OUTPUT:
        RETVAL

# END
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Create FatConst.pm with the following contents.

use warnings; use strict;
package FatConst;
use Exporter;
use DynaLoader;
use Fcntl;
our $VERSION = 1.00;
our @ISA = (Exporter::, DynaLoader::);
bootstrap FatConst::;
our @EXPORT = qw"
    ATTR_RO ATTR_HIDDEN ATTR_SYS ATTR_VOLUME ATTR_DIR ATTR_ARCH
    fat_get_attr fat_format_attr
";
our @EXPORT_OK = qw"
    FAT_IOCTL_GET_ATTRIBUTES FAT_IOCTL_SET_ATTRIBUTES
";
sub fat_get_attr {
    my($fname) = @_;
    sysopen my $F, $fname, O_RDONLY() or return;
    my $o = pack "x8";
    ioctl $F, FAT_IOCTL_GET_ATTRIBUTES(), $o or return;
    return unpack "L", $o;
}
sub fat_format_attr {
    my($n) = @_;
    my $o = "";
    for my $i (0 .. 7) {
        $o = ($n & (1 << $i) ? substr("RHSVDAXY", $i, 1) : " ") . $o;
    }
    $o;
}
1;
__END__
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Create Makefile.PL with the following contents.

use warnings; use strict;
use ExtUtils::MakeMaker;
WriteMakefile(
    NAME => "FatConst",
    VERSION_FROM => "FatConst.pm",
);
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Now compile the module we've created with perl Makefile.PL && make

I have mounted a vfat filesystem to /mnt/s0, let's test reading file attributes with the above module on it. I run this command.

sudo -u oper perl -I./blib/arch -we 'use FatConst; my $d 
= $ARGV[0]; opendir my $D, $d or die; while (my $b = readdir $D) { my 
+$n = $d . "/" . $b; my $err = !defined(my $a = fat_get_attr($n)); pri
+ntf "%8s  %s\n", ($err ? "E" : fat_format_attr($a)), $n; }' /mnt/s0
[download]

And the output is

Setting the attributes (instead of getting them) should be similar and is left as an exercise to the reader.

Update: changed type of ioctl constants from I32 to int, for that's the more correct type, though they mean the same.