Running a simple transistor buffer that has been designed for 9V on 5V runs the risk of distorting the signal, either because the signal hits the rails or because of the misbiasing. Moreover, these simple circuits are designed to run on clean power either from a battery or a well filtered and regulated linear power supply. Running them on a switching power supply is likely to introduce noise. Worse, running these analog curcuits from the same power supply as a digital device will likely introduce more issues. Here are a few suggestions ordered from the simplest:
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Use any pedal that has a buffered bypass. All Boss pedals (in)famously feature a buffered bypass. If you don’t want to bust the bank spending 100 EUR for something that you will mostly use as a buffer, you can get one of these Behringer clones. You can find those for as little as 10 EUR second-hand.
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Use any other device that provides buffering for a guitar input, with a direct out, such as a portable recorder, an audio interface, a preamp, etc. Again, Behringer has these little tube preamps that you can find for as little as 25 EUR second hand.
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Build a simple JFET buffer with a 9V battery supply. JFETs are getting more difficult to find these days, but since this is a boost, you can use any JFET that is reasonably priced (e.g. 20c). Alternatively, you can build a buffer using an op amp.
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If you must run the buffer on the same 5V supply as the Zynthian, I would recommend using a charge pump (e.g. ICL7660/MAX1673) to get from 5V to 9V, and add some power filtering and/or regulation.
I personally use 1 and 2 for both guitar and bass, and I have built 3, but I did not find it too practical. 4 could work but I haven’t tried.