I have not tried Silicon transistors.
I kinda got a fetish for Germaniums because of the great picking dynamics and guitar-volume cleanup I get from them compared to Silicon, so the idea never struck me...
But try it!
The design is pretty much a standard amp sim circuit in the style of the Superbolt, so it should work.
But I suspect you will have better luck with JFet transistors, as that is what normally is used in amp sim circuits, because of the similarity they have in character to tubes.
You probably need to socket the 33k resistors though, to get the bias correct if not using the 103NU71's.
Here is some info from the original source that might shed some light on the subject:
http://apocalypseaudio.blogspot.no/2009/02/apocalypse-audio-thundertone.html