Machon Keter - an organization that studies and encourages finances according to a torah approach - has published an interesting psak regarding the purchase of tefillin.

The question they dealt with was how to relate to holy objects - tefillin and mezuza - that was purchased from someone who does not pay his taxes. Is such a person - a sofer who does not pay taxes - passul or lose his status of being a trustworthy and reliable person (from a halachic standpoint)? Are using such objects considered performing a mitzva via an aveira? can you make a bracha on such tefillin?

Their conclusions were that:
1. a sofer who evades taxes or steals from other people is not passul from writing holy objects like tefilllin and mezuza and his status as trustworthy and reliable remains.

2. somebody who buys tefillin "black" cannot make a bracha on the tefillin he acquired through an aveira. By buying "black" he is assisting in an aveira, and cannot make a bracha, and therefor eit is also prohibited to purchase tefillin like that.  However, if the person already wore the tefillin, bdieved he fulfilled his obligation - the tefillin themselves do not become passul.

If the buyer truly does not know what the seller does regarding the paying of the required taxes, despite being negligent in not clarifying before purchasing, he can make a bracha on his tefillin. And, this is dependent on his knowledge at the time of purchase - even if he finds out later that the seller did not pay his taxes, he can continue putting on his tefillin.
source: Kipa

I am pretty sure that at least 99 times out of 100 a buyer will have no idea if the seller is paying taxes or not and won't even think of asking. It might even be rude to ask, as if you are saying you suspect that he is doing something illegal. The relevant situation might be where you ask for a discount of the taxes for paying cash.