I don't think it is anything about the timing. Although as you say they are similar, and might be used interchangeably, the difference is what 'lot' refers to. 'A lot of books' means many books. 'reading a lot' refers to the amount of time you have spent reading. Without 'of books', the 'lot' changes what it refers to. So - the difference is between the number of books you have read, versus the time you have spent reading them. The first would probably mean you have been reading fast. The second might suggest you have been reading often, but perhaps sporadically, so you have to keep looking back to remind yourself of where you were up to.
I would also not refer to reading as a habit - the word 'habit' now has more of a negative connotation, such as a smoking habit, or a habit of picking your nose. It can also be used for things that you do for no reason, such as 'I normally just walk down that road as a matter of habit'. It would be unusual nowadays to use it for something recreational such as reading.