It is possible to say "books" without an article because the indefinite article for plural countable nouns does not exist i.e. zero article. Like you said, here you need "the" or another determiner because we are referring to an identified and specific group of books. On the other hand, "pen" is a singular countable noun and so always needs an article or other determiner. A descriptive adjective like "red" is not a determiner. I always tell my students not to leave singular countable nouns alone - it's tough for them!

Thank you for your kind comment, Mr Dimitris Proko!

The best possible and easy answer is to say: "The Books are above the desk" As for your second concern, it is better to say: "That is his red pen" ( however saying | The red pen is his is also correct) Hope that might clarified your questions!