Since my array is 2d and each row has a different number of values (columns), doesn't it mean it will require a lot of programming overhead defining the templates?

It can be as simple as representing each row by an integer, which holds the number of numbers in that row, and then the row in fixed with (for example always 4 byte per number).

But that all depends on how flexible you want the data retrieval to be, how robust it must be etc.