Unless the SWR is broken, it isn't generating spurious signal on its own.
It comes from somewhere, probably VLF from string movement over the pickups.
I have no experience measuring sub-harmonics, so can't comment.
What I can really see causing piston action, is moving the strings about over the pickup.
I always thumb-damp my B-string whenever I'm not playing that string.
I can see where motion would induce VLF signal.
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This preamp evidently does not have the reputed rolloff, as it is only down -5dB at 12 Hz.
On the flip side, my Sansamps are reputed to have a steep rolloff from 80 Hz, which I have not yet measured.
My various PLX have a 30/50 Hz filter which is useful, but my new Prolite2 does not.
Looking at the FDECK HPF, I see it has a 12db/octave slope with the lowest corner at 35 Hz.
Whenever I play at high power, it is with the PLX and filters engaged.
My T39 unloads below 42 Hz, and the T48 around 35 Hz, so I keep the filters in place.
Again, this has nothing to do with there being 'something wrong' with the SM400. It is what it is.
This is not a 'preamp' issue, and measuring the preamp's frequency response coming out of the effects out or whatever will tell you nothing.
Per your example, think of an integrated bass amp as just a preamp combined with a power amp. Just like your PA type power amps having low end control (typically a limited low pass filter control with a couple fixed settings), the amplifier sections of integrated amps have various low end control circuits (hi passing and low end voicing that is not 'user adjustable' in most cases).
The SM400 is somewhat unusual in that it produces lots of deep, sub-bass low end. This was actually part of its 'marketing spec' also... full 20hz to 20K response out of the entire system. This again was not a very good idea since the vast majority of speaker cabs can't use much under 40hz. Many of us used an external hi pass set at around 35 or 40 hz back in the day with that head. Worked nicely to increase the efficiency/volume of the rig for sure.
Where you REALLY get into trouble (IMO and quite a bit of IME) is using this head with a cab that actually has high sensitivity way down low, like the Acme. At even moderate volumes, that is a wonderful formula for cone creasing, and also low sensitivity of the entire system, since SO much energy is used to create that super low, 30hz and under type output.
Of course, the sub bass comes originally from the instrument. There are some unique on-board preamps like the preamp that Pete Skjold uses that have adjustable hi passing (cool idea.... keeps those front of house guys from going nuts with the bass tone in the subs). Otherwise, with an amp with too much low end extension, an external hi pass like the FDECK works quite well.
The FDECKIII has a fixed 35hz 12db per octave roll-off that is not adjustable, and then an additional 12db per octave adjustable roll-off, from 35 hz (so you can have a 24db per octave roll-off at 35 hz) all the way up to 120hz or so (i.e., fridge emulation or whatever).
The Shuttle Max heads had a pretty cool 'low end filter' that was basically an adjustable hi pass filter combined with low end boost (since the ear hears those lower frequencies less efficiently). I believe its range was from 36hz when off to 32 hz when fully engaged. LOTS of low end within that range!
