Nibot,
I strongly suggest you read Noise and Fluctuations by D.K.C. MacDonald. It has lots of great discussions related to thermal noise. That's where most of this answer comes from.
You are probably used to the Fluctuation Dissipation Theorem (FDT) written in a form similar to the way Nyquist derived Johnson noise on a resistor:
$$
<\delta V_f^2> = 4RkT df
$$
Which is the variance in the Voltage squared, in terms of $R$ the resistence, $kT$ the temperature, and $df$ the measurement bandwidth. (Alternatively divide both sides by $df$ and the quantity is the power spectral density).
But there is another form of Nyquist's theorem for when $hf \approx kT$, i.e. valid in the quantum regime.
$$
<\delta V_f^2> = 4R\left( \frac{hf}{2}+\frac{hf}{e^{hf/kT}-1}\right) df
$$
You should be able to convince yourself that this reduces to the standard Nyquist formula in the appropriate limit.
Using this form of the theorem, and considering a charged particle which oscillates in vacuum, there is a damping back-reaction of the electromagnetic field given by the Larmour formula:
$$
\vec{E} = -\frac{(2\pi f)^2}{6\pi \epsilon_0 c^3} \dot{ \vec{p}},
$$
for the electric field $\vec{E}$ and dipole $\vec{p}$. So with analogy to the Nyquist formula, $<\delta V^2_f>$ describes the electric field fluctuations, and $R=\frac{(2\pi f)^2}{6 \pi \epsilon_0 c^3}$. Surprisingly, plugging this into the quantum Nyquist theorem reproduces the blackbody radiation spectrum! The FDT never ceases to amaze!
Note that my quantum FDT includes a zero point energy term, which is a bit controversial, because it also predicts a blackbody spectrum which has a zero point energy term, which can't be observed directly.
Now, I must admit I tried and failed to derive the shot noise formula from the blackbody spectrum with the zero point energy term added, but because shot noise is often attributed to zero point energy fluctuations of the EM field, it feels like this represents the same thing physically. I think my math skillz just weren't cutting it.
I guess one thing to realize is that these optical measurments are working in the $hf\gg kT$ limit while usually thermal noise is concerned with the opposite limit. But imagine an interferometer working with 10 $\mu$m light, where the room temperature thermal spectrum is large. This interferometer would be primarily concerned with thermal fluctuations entering ports, rather than quantum ones!