o(1) in time complexity of number field sieve
Summary: it is common, and arguably safe, to assume that the $o(1)$ term is positive, and take it at zero, in circumstances where the formula is then used to estimate a lower bound of the ratio of work for larger value of $n$ to that for smaller values of $n$.



The formula given, with $o(1)$ term, gives the complexity of NFS. If modified by assigning a real value (say, zero) to the $o(1)$ term, it yields a function of $n$ without unit, thus insufficient to calculate the time (or effort, or cost) needed to run the algorithm for a given $n$. The $o(1)$ term happens to encompass the very order of magnitude of the cost (as a consequence of the outer exponential and the positive exponent to the $\log n$ term).

However, a common and legitimate use of that formula is to evaluate how the effort to run the NFS scales with $n$, by computing the ratio of what the formula gives for different values of $n$ (and taking the base-2 log for a security variation in bits). In that sense, it makes sense to ask which value of $o(1)$ should be used for a given $n$.

I don't know, and likely that depends on the variant of NFS (which also has a huge influence on $C$), and the hardware at hand.

However, a common approach is to hypothesize that this $o(1)$ term is positive, and take it as zero when extrapolating how larger $n$ needs to be, thus (if the hypothesis is correct) erring on the safe side from a key-holder's point of view.



Addition commenting the self-answer: an example of the practice in the previous paragraph is the formula given by the NIST in Implementation Guidance for FIPS PUB 140-2 and the Cryptographic Module Validation Program (updated August 1, 2016), computing the conventional bit strength $x$ of an RSA public modulus of $L$ bits as
$$x\;=\;{1.923\times\sqrt[3]{L\log(2)}\times\sqrt[3]{(\log(L\log (2)))^2}-4.69\over\log(2)}$$
which is obtained by


straightforward transformation of the GNFS complexity formula using $C=\sqrt[3]{64\over9}$ rounded to 4 significant digits;
ignoring the $o(1)$ term, thus obtaining an $x$ such that $2^x$ is an estimation of work in unknown unit;
solving the above issue by introducing the additive constant $-4.69$ (which really is a multiplicative constant of $2^{-4.69/\log(2)}$ on the involved work $2^x$), determined so that when $L=1024=2^{10}$, the result obtained is $x=80.000\dots$, because that fits the FIPS 140-2 normative context, and anecdotal evidence suggests that the cost of breaking common 80-bit symmetric cryptography would be smaller than the cost of factoring a properly generated 1024-bit RSA modulus.


That formula thus arguably errs on the safe side from the key-holder's point of view if used to estimate the security given by an RSA modulus of $L\ge1024$ bits properly generated from true randomness, under the assumption that GNFS roughly as practiced now remains the best factoring algorithm.