Mr Bond may be fond of
Theory or things that require you to deduce and think about.
He may not like
Things that have a rigidity around them or a physical presence. Physics deal with how objects interact with the space and there is also the rigid body we use in calculations. Biology aka living matter which have a physical presence and so do rocks.
About the pen and paper, here is how I interpret it as. The pen's use is to write and we write on papers. So unless a pen is being used to write, it has no significance other than aesthetics. When it is used on paper, it leaves a physical trace i.e the ink on the paper which is why he does not like it.
Another interpretation can be
Mr Bond likes aesthetics. To some, mathematical formulas and chemical formulas look beautiful. So does a pen. Whereas Biology, Physics and paper are fascinating but aren't exactly what one would consider as beautiful (speaking in terms of the strictly mathematical geekiness here. And Physics problems have math in them. Also look at a paper under a microscope, it's not so smooth as it seems)
Attempt 2 The Correct Answer
Mr Bond likes things which contain total number of letters that are perfect squares. Math = 4 , Chemistry = 9 , pens = 4 letters each which are perfect squares of 2 and 3. Whereas Biology = 7, physics = 7, rocks = 5, papers = 6 which are not perfect squares of anything. This can also be interpreted as Mr Bond likes words with a total number of letters that have a whole integer value as their square root i.e 2 and 3 as stated above.