Should I mention in my letter of recommendation that my student has bad handwritting? A student I taught is really a good student but writes like he is writing with his wrong hand.

The college where I teach requires every one to administer a subjective final exam for 60% of the grade. Its a 3 hour exam and people usually fillout a 30 page booklet. I know many lecturers gave him bad grades because they were too impatient to read his answers they gave him B+ or a B when he deserves at-least a A. I know this cause I taught him Data structures using C and he performed very well while he got a mere B grade in a C language course.

Should I mention this in my LOR or will mentioning this have some bad consequence for him.

I can easily grade 3 students in the time I grade his one paper. So I can imagine how some universities could see him as a liability.
I would not mention this no, this should not have any consequence to the students application, it may be a little out of place. It would be worth advising the student to inform any future places of study about his handwriting he may be able to get some alternate support with regard to exams. 

I would not see this student as a liability, just maybe needing a little extra support in this area, it is fair for an examiner to not spend ages marking one students paper due to bad handwriting, so long as they give it a fair go and a good effort.