You are kinda cryptic in your question, pick a question answer set:
Q: How are the special attack and special defense scores calculated in Gold/Silver?
A. The same way that the special score is in the previous games, except that the base value for special attack and special defense now may be different. That decision was made on a per monster basis.
Q: Are there two deter (gene) values, one for each of special attack and defense, or is it totally based off the old one, or something else?
A: The only thing that has been modified (and not in all cases) is the base value. This means that the special gene is used on both special attack and special defense, and that the bonus from stat EXP given to your special score in the older games is given to both special attack and special defense in the new one.
What this means is that you have the same stat EXP counters as before, and the results are applied the same, except that one of them (special) counts for two stats.
What I don't know is how it calculates how much stat EXP you recieve when you take out a monster with differing SpAtt and SpDef. Do you recieve an average?
Hope this helps, if this isn't what you were asking, ask again...