I'm not sure how strict your interpretation of number theory is but Sofia Gubaidulina used the [Evangelist][1] and [Lucas][2] series in some of her compositions.

I don't know if this is entirely relevant to your question but I have started writing functions in C to develop themes with the techniques I have used for years with paper and pencil. Because of the ease with which it can be done with a computer I have started using random numbers to introduce a slight variation into the functions. The random numbers are produced by taking the square root of numbers such as 15 to 48- 54 decimal places and decimalising the numbers after the decimal point, using modulus 3 or 2 if only a slight variation is wanted. Sometimes I use the Euler-Mascheroni Constant.

Another technique I use is convert a theme I like by another composer into numbers and use those in various ways.

What I do is not algorithmic as I copy the developed themes onto manuscript paper and then compose normally. 


  [1]: http://oeis.org/A001060
  [2]: http://oeis.org/A000032