The statement "I use Perl for all programs of less than a thousand lines" does not, to me, say anything about using it in longer programs. It just says "For short, quick programming, I like Perl." There is no "but for long programs, I like <language>."

Nothing about that statement indicates to me that the use of Perl for short programs in any way precludes using Perl for long programs. Therefore, use Perl in situations that call for it, be they short or long, complex or simple.