Your latter idea, assigning ID numbers to people, having "number,name" in one file and "date,number(s),hours" in the other file, is definitely the way to go. This is called normalizing a database -- basically, don't store a piece of "mutable" data in more than one place.

For that matter, don't store more than one name/person-number in a single "hours" record: i.e., it should always be just "date,person_number,hours", one person mentioned per row.

As for better suggestions, try actually using a relational database (e.g. mysql), where this sort of thing is quite natural and easy. (But that's not essential -- for something on this scale, you could just as well use perl hashes to provide the same functionality without breaking a sweat.)