Think about the overhead involved. Here is my brief analysis:

open(INFILE,"cat textfile |")
while(<INFILE>) {...}
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This opens a type of file handle commonly known as a pipe. It spawns an additional process, complete with a duplicate set of environment variables and memory management requirements. The OS must now swap memory back and forth between Perl and cat.

open(INFILE,"textfile")
while(<INFILE>) {...}
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Perl opens a file handle directly to the file. No other processes are started.

system("cat textfile | filter.pl")
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Perl invokes the shell which invokes cat and another instance of Perl! Plus the shell still has to open a file handle for the output of cat / the input to filter.pl

Result: All three methods require a filehandle (aka a fileno, or a file descriptor) and two of the methods have the additional overhead of multiple processes. Use the second method and avoid all that.