I'm not sure how strict your interpretation of number theory is but Sofia Gubaidulina used the Evangelist and Lucas 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 withon 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 and sometimes an array of random numbers of 1 and -1 if I change something up or down - e.g. when I use the mean between numbers and some are odd.
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.