Disclaimer: I struggle with this question myself a bit. I think I have something to add that may be helpful to you but it isn't going to be a superpolished answer and it might be a little unclear at times.
Consider
$$
H = \int \hbar \omega b^{\dagger}(\omega)b(\omega) d\omega
$$
We see that, since $H$ has units of energy, $\hbar \omega$ has units of energy, and $d\omega$ has units of frequency we can see that $b^{\dagger}(\omega)b(\omega)$ has units of inverse frequency, that is $Hz^{-1}$.
In this form it is clear that $\hbar \omega b^{\dagger}(\omega)b(\omega)$ represents the total energy per unit frequency. That is, we can see that $\hbar \omega b^{\dagger}(\omega)b(\omega)$ is like a power spectral density for the photon field. If you integrate over some frequency range $[\omega_1, \omega_2]$ you get the total energy contained in that bandwidth. $b^{\dagger}(\omega)b(\omega)$ is then some sort of excitation spectral density. Again, if you integrate you get the total number of excitations in some bandwidth. If $b^{\dagger}(\omega)b(\omega)$ is the power spectral density of the signal then $b(\omega)$ is the signal itself, it is related to the square root of the power spectral density. Thus it has units of $Hz^{-\frac{1}{2}}$. This unit comes up often in signal processing. We talk about "Something per root Hz" when we want to discuss a power spectral density which is scaled to have units comparable to the amplitude of a signal rather than the power in the signal.
Ok, so to recap $b(\omega)$ has units of $Hz^{-\frac{1}{2}}$. We now consider the "in" field:
$$
b_{in}(t) = \int e^{i\omega t}b_0(\omega) d\omega
$$
First notice that $b_{in}(t)$ is a function of time not frequency. This is because frequency was integrated over. Next, you've noticed that $b_{in}(t)$ has units of $Hz^{\frac{1}{2}}$ now, or $s^{-\frac{1}{2}}$. So I think this should first and foremost simply be thought of as an integral over bath operators. In the description with $b_0(\omega)$ we have split thing up by their frequency modes, somehow we've already done a Fourier transform. $b_{in}(t)$ captures the integrated signal which is the composition of all of those modes into one operator.
But there is an important point which has not been discussed yet. The input-output formalism is often considering photons inside of a cavity described by some cavity operators $a$ which are coupled to some continuum modes outside of the cavity, $b(\omega)$. Let's think about the electromagnetic fields inside and outside of the cavity.
Inside the cavity there are standing wave modes of light. Note that the standing wave is composed of a left travelling wave and right travelling wave. There is no spatial translation of the energy in the cavity. You can think of the cavity as a box and the total energy in the box is $\hbar \omega a^{\dagger} a$ (no funny integral, now $a$ is dimensionless in contrast to $b(\omega)$ which has units of $Hz^{-\frac{1}{2}}$ or $b_{in}(t)$ which has units of $s^{-\frac{1}{2}}$).
However, in free space it is possible to have a travelling wave in one direction without also having the travelling wave in the other direction. That is, it is possible to have waves carrying energy in a particular direction, we can talk now about energy flow.
Both in a cavity and in free space the electromagnetic field must satisfy the Helmholtz equation. The difference is that the boundary conditions are different. For the cavity the boundary conditions give you a discrete density of states and standing waves while in free space you get a continuum of modes - some travelling left and some right.
$b_{in}(t)$ sort of represents the full solution to the Helmholtz equation in question while the $b(\omega)$ are the individual frequency components of $b_{in}(t)$.
The interesting bit is that in addition to asking about the total energy in the electromagnetic field (the Hamiltonian integral above) one can ask about the intensity or flux of energy passing through a surface. Now that we can talk about flux we can think of the $s^{-1}$ unit on $b^{\dagger}_{in}(t)b_{in}(t)$ as being related to the energy passing through a surface per unit time.
For example, if we detect the output field $b_{out}(t)$ on a photodetector (which we often do) then we need only consider the energy in $b_{out}(t)$ in a narrow bandwidth (the detector response band). In that case the intensity is
$$
I(t) = \frac{c\epsilon_0}{2} |E(t)|^2 = \frac{c \epsilon_0}{2} \frac{\hbar \omega}{2V \epsilon_0} b_{out}^{\dagger}(t) b_{out}(t) = \frac{\hbar \omega c}{4 V} b_{out}^{\dagger}(t)b_{out}(t)
$$
We see that the units work out. There is the pesky mode volume $V$ showing up which came from quantizing the electric field in the continuum.. if things are handled properly one can make this go away. But the point is the factor $\hbar \omega$ gives us energy in the formula, the factor $\frac{c}{V}$ tells us something about the geometry of the travelling wave. $V$ might be related to the cross section of the beam. Then with all of this it is reasonable to say that $b_{out}^{\dagger}(t)b_{out}(t)$ is in fact telling us about the number of photons falling on the detector per unit time.
Anyways, this answer has sort of gotten away from me. My advice would be the following. First, realize that this formalism is working in the Heisenberg picture. Get comfortable with that. To help get comfortable with that it may be beneficial to try to translate everything into a purely classical description. In particular there is in fact very little quantum about the input output formalism except the fact that the operators all have funny commutation relations, so stripping away the quantumness might help.
Next I'll just give a list of all the things that might be confusing here having to do with the relationship between frequency and time.
- Heisenberg picture
- Fourier Transform
- Power spectral density
- amplitude vs energy/power
- energy vs intensity
- discrete vs continuous density of states
Anyways, I hope this is able to help a little bit. Sorry it's so scatterbrained.