If file is corrupted, split /\t/,$_ will return something else and some of the array elements may eventually become undefined. Perl will throw a warning if you use warnings when you try to do something with such elements. You may want to check elements using defined, but this can slow down your program.

When you are working with TONS of data, it can be useful to try SQL (sqlite, for example).

Yes, you will be able to access all of your data using array references. Data::Dumper and x command in debugger are useful when you have troubles with acessing some data strictures in Perl.