1) Sampling rate:
Imagine my algorithm requires a fixed sampling rate (e.g. fs = 44100), block size (e.g. 2048 @ fs = 44.1k) and hop size (e.g. 1024 @ fs=44.1kHz). I understand that I can specify a preferred block and hop size, and even return false in the initialization function if the host specifies something else. But, what about the sampling rate? Specifying a required block/hop size (in samples) is not really useful if the sampling rate is not known.
I'm afraid the samplerate is one thing your plugin has no control over. It must accept whatever's supplied in the constructor, and can only then return false on initialise if the rate is unsatisfactory.
Note that the plugin's block and hop size can depend on the samplerate, they don't have to be hardcoded -- if the reason you want to fix the samplerate is in order to have known block and hop size in physical units (i.e. seconds), you may be able to do it the other way around -- calculate the block and hop size on request based on the samplerate.
I realise I can save the value of inputSampleRate to a parameter
You don't actually need to save it, it's stored for you in the Plugin base class. (This is probably bad form in terms of software practice, but still)
Is there no way to re-sample the audio before it is chopped into blocks?
2) Time-domain filtering:
Is there any way to apply a time domain filter first, and then get the input in the frequency domain? Just hoping to avoid having to compute the DFT inside the plug-in itself.
No, the frequency-domain input is essentially a convenience option for plugins simple enough to be happy to work from STFT data without having to have too much control over it (the host also controls the window shape, for example). More sophisticated plugins will need to work from time-domain data.
In hindsight I wish we had put a generally accessible FFT implementation in the SDK on the plugin side, as well as in PluginInputDomainAdapter on the host side -- there are now many, many duplicates of FFT functions in Vamp plugins out there! Perhaps it's not too late to add it, even.
3) Sonification (sonic visualiser):
In sonic visualiser I see that some output types can be sonified (e.g. clicks at detected onsets). If the output of my plug-in is a continuous per-frame frequency value (in Hz), is there any way to sonify the output in sonic visualiser, e.g. with a sinusoid that follows the frequency of the output?
No, Sonic Visualiser only contains a MIDI-note-based sound generator that uses sampled sounds. Again though, I know quite a lot of people would find this useful. Maybe I should look at it...
Sorry to have such a negative list of responses for you. The positive side is that it looks as if you've understood the SDK and its limitations pretty well...