It’s very application dependent. Spectrum analyzers are typically performing real-time estimates, so using FFT methods is more efficient than modern spectral estimation methods, since most modern estimates need to invert a correlation matrix, which is $\mathcal{O}(N^{2})$ if you use a toeplitz estimate and can use Levinson recursion.
One place where spectral estimation found a niche was in SAR imaging. You could form the image, transmit it, then post-process it via spectral estimation. It’s a little bit easier to do spectral analysis with spatial signals (eg DOA/Beamforming) because you often don’t have as many samples as you would in a temporal signal.
There are two main approaches to spectral analysis: filterbank and model based approaches. Classical Fourier methods (that you refer to as FFT based methods), are based on non-adaptive filterbanks. Modern filterbank methods are based on adaptive filterbanks, ie RFB, Capon, etc. Then there are also finite-dimensional models like AR/LP, MUSIC, etc. Some of these techniques also have the ability to be computed via FFT, although a bit more indirectly. The idea behind these modern methods is that they have better statistical properties as most of them are both asymptotically unbiased and consistent, unlike classical Fourier methods.