The Jaynes-Cummings Hamiltonian, if we are being historical purists, refers specifically to the interaction between a single two level system and a single harmonic oscillator mode. This is a toy model for the interaction between a single atom and an optical cavity.
One can generalize this Hamiltonian in many ways. As you point out, we can include many atoms. We can also allow the atoms to have more complicated level structures than just two levels. We can allow the atoms to move through the cavity mode (so that $g$ is a function of atomic position $g(\hat{x})$). We can also include many longitudinal and transverse cavity modes.
The generalization you suggest of allowing the spins to interact with each other is a valid extension which has not been wholly unexplored. Why is it not typically included?
It should only be included if it has a big impact on the physics. In many atomic physics experiments the direct interaction between neutral atoms is very very minor. So minor that, even at a perturbation theory level, it just doesn't affect the physics that is observed.
One case where direct interactions between the spins of neutral atoms is when the atoms are Bose condensed. In this case the density is very high that atom-atom collisions can affect the physics. In the case of spinor BECs this physics can be spin-dependent.
Another case is in the case of highly magnetic atoms whos magnetic moments can interact at a longer distance.
Another case in which direct spin spin interactions are significant is the case of Rydberg atoms.
It's also worth mentioning that the model of a cavity interacting with multiple atoms can, in certain regimes, give rise to effective spin-spin interactions between different atoms. Sometimes it is said that the "direct" interaction you are curious about is mediated by real photons being exchanged between the atoms while the effective spin-spin atoms to which I am referring are mediated by virtual cavity photons.
edit: Short version: One pedantic answer is that there's no spin-spin interaction because then it wouldn't be the Jaynes-Cummings Hamiltonian! The Jaynes-Cummings Hamiltonian should only have 1 atom anyways! The more serious answer is that, at least in neutral atom experiments where this model is studied, the spin-spin interactions are typically so small that they don't affect the physics at all. But, that's not to say it's impossible to develop experiments in which direct spin-spin interactions between neutral atoms DO affect the physics.