I can attest to this first hand. I had a cafe bike.
I bought (and still have) my first bike 4 years ago. It was a tired 1980 R65 for $1900.
I bought clip on handle bars and a cafe seat then sole the instrumentation console and put on an acewell all in one speedo/tach.
I don't like the idea of ruining a bike so that's as far as I went with it.
Fast forward to now and I hate my uncomfortable seat, sold the handlebars for something less aggressive which amounts to R90s bars. My bike sucked to ride but it looked cool.
r90S style bars and a slightly more comfortable seat and I love my bike now.
The problem I see with the recent obsession with cafe bikes is that people have taken it further than a simple handlebar & seat change.
I see bikes all over the web & instagram/social media where builders are buying a decent rideable bike then doing the following:
-low bars
-cafe seat
-rear set pegs
-removed airbox and relocated battery
-new headlight/turn signals & taillights
-hacked front fender and removed rear fender
-offroad tires
-lowered rear shocks
-lowered(compressed) front shocks
They took a comfortable bike with a nice seat, nice riding position, decent shock travel and decent tires and removed all of that. Sure it looks cool, it does....but the issue is that the person who pays $8k for it will ride it for a week and realize it's the most uncomfortable thing ever and then try to revert back to the baseline or just stop riding and sell it.
Everyone I know who had a cafe bike reverted back at least a little bit and the reason is because they suck to ride.

Now when I see a scrambler/cafe/whatever bike with no suspension travel and dualsport tires I feel bad for them. They may be fooling some people but they're not fooling me with that uncomfortable weekend queen.