John T's answer is the way to go for hex conversions, but you can also do them this way (which can be used for other bases as well):
$ hexval=0x59999
$ hexval=${hexval#*x}
$ echo $((16#$hexval))
367001
Demonstration:
$ echo $((2#1011010))
90
$ echo $((8#1776))
1022
$ echo $((23#mmmmm))
6436342
Edit:
#!/bin/bash
base=16
while read -r val
do
val=${val#*x}
echo $(($base#$val))
done < inputfile > outputfile
The only advantage over John T's answer is that this one can be easily adapted to convert other bases to decimal. His is quite a bit faster.
This gawk command seems to be a little faster than John's shell version:
gawk --non-decimal-data '{printf "%d\n",$1}' inputfile > outputfile
It's about the same speed as your Perl command. Why not just use it?
By the way, the last part of your Perl one-liner can be replaced by the -l option:
perl -lpe '$_=hex'
Another note: Typically the pipeline you show in your question would be written as:
util < file1 > file2
or, if cat represents placeholders, then dummy names should be used:
prog1 < file1 | util | prog2 > file2
then you won't have people complaining about useless uses of cat.