Guitar Cabs and speakers are the limiting factor when doing this. I feel comfortable using my 4x12 Greenback Cab, as it has enough Headroom for the 30-ish Watts a clean JTM puts out. (I know it's not only the wattage, but also the frequencies that can kill speakers, but I keep the Amp's Volume at 2-3 max in that case).
You're pretty safe running a JTM45 into a 4x25W cab, the ultra low end response is pretty limited in a GB anyway. I got the best (well, to me) results using a single M65 Creamback, though indeed - I'm not cranking the amp, I generally want squeaky clean or close on bass.
2. Using the JTM with IRs. I have a crappy Harley Benton Attenuator that I don't use much. But it works as a Load Box with DI out, so I can send the signal of the JTM to my Interface and use a Convolver plus some Bass Cab IRs. Sometimes it's a good sloution to use a mix of the Mic'ed Greenback Cab and the DI Signal plus IR.
...actually, the Harley Benton is crap but for that one use case it makes sense; it will likely reduce some of the transients and flatten the signal somewhat. That might actually be beneficial in this scenario. Heck, I've got a PS1 for bench duty, I might try that just for fun!
3. Going purely Digital (Blasphemous!

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Sometimes I use Plugins inside the DAW. I have a paid Ampeg SVT Plugin, that I got on sale for 30 Euros. I won't pay more for a piece of Software which may be obsolete or unusable in a few years.
Agree, exactly why I prefer not to rely on specific plugins. I tried a sim long ago as it happens and it sounded OK, but I wanted something I could play in the room with zero latency, too.
I plug direct into the interface and use one of two Ampeg modelers on the computer… a B15N and a VST… and I love it. Tons of control, you can switch amps after the fact, or add virtual pedals.
Yes, for a while I did that, too; two mics on the cab and snag a DI capture at the same time. It was about then that I decided it was getting way too complex and I had to go back to basics. Enter the SansAmp. Those things have been used for ages in studios and are heard on tons of albums out there, including high profile artists. Why? Because they never deliver the greatest tone, but almost always a usable one. Consistent, reliable, doable. Still, sometimes I have a number where I think to myself that something else would be better. Stealin' by Uriah Heep, for example. One Of These Days or Have A Cigar by Pink Floyd.
Micing a bass amp is a PITA.
So I'm not alone in this, good, haha!
Micing a bass amp is a PITA.