In the european-union, this is governed under Article 79 of the Union Customs Code (UCC). Your question can be divided into two parts which I will address separately.
Yes, there will be a customs debt
Article 79(1)(a)
A customs debt on import shall be incurred through non-compliance with [...] the obligations laid down in the customs legislation concerning the introduction of non-Union goods into the customs territory of the Union, their removal from customs supervision, or the movement, processing, storage, temporary storage, temporary admission, or disposal of such goods within that territory.
This means that even if goods are seized and never enter legal circulation, a customs debt is still incurred the moment the smuggler violates customs regulations by attempting to bring them into the EU without compliance.
Article 79(3)
The debtor shall be: (a) any person who was required to fulfil the obligations concerned;
(b) any person who was aware or should reasonably have been aware that an obligation under the customs legislation was not fulfilled and who participated in the act which led to the non-fulfilment of the obligation;
(c) any person who acquired or held the goods in question and who was aware or should reasonably have been aware that an obligation under the customs legislation was not fulfilled.
Bob, the smuggler, is liable for customs duties under these provisions, as he knowingly violated import rules.
The method of valuation will vary
Regarding your question on the value of goods, there are a number of articles that deal with this question. In particular, these can be found in Chapter 3 of the Contents titled:
Value of goods for customs purposes
In order to value the customs debt, the seized assets must be valued. This is not always a straightforward process (as you allude to in the question). This is dealt with by the above articles. The exact method of valuation depends on the good in question.
The simplest case relates to goods which can legally be exported:
Article 70(1)
The primary basis for the customs value of goods shall be the transaction value, that is the price actually paid or payable for the goods when sold for export to the customs territory of the Union, adjusted, where necessary.
This seems to match your intuition regarding goods like cigarettes. But this does not help with illicit goods (eg ivory). Instead, we must refer to Article 74:
Article 74(1)
Where the customs value of goods cannot be determined under Article 70, it shall be determined by proceeding sequentially from points (a) to (d) of paragraph 2, until the first point under which the customs value of goods can be determined.
As illicit goods cannot be valued under Article 70, this means that they must be valued using the process set out in paragraph 2:
Article 74(2)
The customs value, pursuant to paragraph 1, shall be ...
...
(d) the computed value, consisting of the sum of:
(i)
the cost or value of materials and fabrication or other processing employed in producing the imported goods;
(ii)
an amount for profit and general expenses equal to that usually reflected in sales of goods of the same class or kind as the goods being valued which are made by producers in the country of export for export to the Union;
(iii)
the cost or value of the elements referred to in point (e) of Article 71(1).
I have removed sections a, b, and c from the above as they relate to identical or similar legal equivalents. Assuming there isn't a close enough proxy good, section d outlines the means of valuing an illicit good.
Finally, in the unlikely event that the illicit good cannot be valued using any of the above, Article 74(3) allows for the use of data to ascertain the goods' value as long as this is done consistently with (a) the agreement on implementation of Article VII of the General Agreement on Tariffs and Trade; (b) Article VII of the General Agreement on Tariffs and Trade; (c) Article 74. This means that the black market can be used as a reference in accordance with the above (but Article 74(3) will only invoked if all other methods of valuation above fail).
