Besides using a too small value for the radius of the Universe — which is in fact some 46 billion lightyears, or $R_\mathrm{Uni}\sim4\times10^{28}\,\mathrm{cm}$ — I think you've just made a simple calculation error (my guess is mixing SI and cgs units):
Your result for $n_\gamma$ ("$1.64\times10^{17}$ photons") is a number, whereas in fact the result should be a number density, measured e.g. in $\mathrm{cm}^{-3}$. This value should then be multiplied by the volume of the (observable) Universe.
Photons $\simeq$ CMB photons
The number of photons in the Universe is dominated by the CMB photons, by over two orders of magnitude (see this answer for a discussion of the Universal photon background). Each $\mathrm{cm}^3$ of space holds roughly $n_\gamma = 410$ CMB photons, which I estimate from observations in that answer, but which is indeed also what I get with your own calculation.
If you include all photons — not just CMB photons, but also radio, IR, optical, etc. — the result is $n_\gamma\simeq413\,\mathrm{cm}^{-3}$).
Hence, with a volume of $V_\mathrm{Uni} = 4\pi R_\mathrm{Uni}^3/3 = 3.5\times10^{86}\,\mathrm{cm}^3$ — the total number of photons is
$$
N = n_\gamma V_\mathrm{Uni} = 1.4\times10^{89}\,\mathrm{photons}.
$$
As has been commented above, the number of photons is not really conserved. However, the amount of CMB photons that has been absorbed since they were emitted is actually negligible. The only interactions of these photons that alter their state is scattering on free electrons after the Universe was reionized (which happened 0.5 to 1 billion years after they were emitted). The optical depth to this so-called Thompson scattering is $\tau = 0.066$ (Planck collaboration 2015), so the fraction of CMB photons that have scattered is $1 - e^{-0.066} = 0.06$. But this process doesn't remove any photons from the budget, it only polarizes them.