For what its worth, St. Thomas Aquinas uses the following:
- For deed, actus and actio, the latter seeming preferred, at least as per ST I-II, Q. 18, Art. 1.
- For good, bonum/-a, and for bad, malum/-a.
Actiones are said by St. Thomas both bonae and malae, depending on... well, I won't spoil the book for you. Examples:
Ergo actiones humanae secundum circumstantias sunt bonae vel malae (Ibid., a. 3 s. c.)
Non ergo secundum finem dicitur actio bona vel mala. (Ibid., a. 4 arg. 2
But I fail to quickly find a place where an actio is said bona or mala without the mediation of the verb esse. Instead, I found a plain actus bonus as the subject of a sentence:
Omnis actus bonus concordat rationi et legi aeternae (Ibid., q. 21 a. 1 co.)
Actus bonus is also used by Aquinas in De Malo, and apparently by Okham.
Actus meaning deed, as for I could research quickly, doesn't seem to be Classical (its meanings, according to L&S being much more specific). Among the words listed by L&S meaning deed I've been able to find, these are the relative maximum frequencies:
- Actum: 14K, with a lot of law specific meanings increasing the number
- Factum: 25K, also mixed with other meanings
Actio gives 1.6K and is not listed as meaning deed, but the dictionary entry includes act and action among its meanings.
Unfortunately, after a quick search, I haven't been able to find neither acta nor facta qualified as good or bad in Classical texts.
Conclusion: after this quick (and blatantly non-exhaustive) research, I'd go for actus bonus in ecclesiastical/medieval Latin. As for classical Latin, I'm inclined to think there is no closed expression and a circumlocution is to be preferred (e.g., avoid talking about good deeds, by using things like to act well, do good, etc., not sure witch one, though)