IMO, an intelligence agency would be more likely to invest in other methods (algorithm implementation weaknesses, software bugs, insider access, etc), due to the higher liklihood of sucess.
That said, it's interesting to note that the NSA is moving towards "post-quantum" cryptography[2], under the assumption that suitably powerful quantum computers will be, or have been, built. Whether the NSA already has such suitably powerful quantum computers is anybodys guess.
[1] https://en.wikipedia.org/wiki/Key_size#Brute_force_attack [2] https://www.nsa.gov/ia/programs/suiteb_cryptography/