Characters' original forms that have no independent usage
Generally speaking, it is quite difficult to determine the pronunciation of characters which are pictograms or ideograms without resorting to deduction, inference, or secondary evidence. 《說文新證》 does not go into detail what it means by


  古文字未見單獨出現的囗字


but we can refer to its entry of 「丁」


  甲骨文丁字，或謂象釘形、或謂象城邑、金鉼、人顛頂。以「正」字甲文多从「囗」、金文多从「丁」來看，丁、囗實爲一字，皆城圍之象。


to deduce that the text probably means that there is no independent usage of 「囗」 which refers to the word 「圍」; the independent usage of the original shape 「囗」 is now written as 「丁」, originally referring to a word now written as 「城」 (Baxter-Sagart OC: /*[d]eŋ/) with fourth heavenly stem (/*tˤeŋ/) as a phonetic loan.

I wouldn't think too much of the pronunciation 「圍」 (/*[ɢ]ʷə[j]/) for 「囗」, which does not appear to have any direct evidence in ancient inscriptions; rather, 「囗」 (walled city) as a component has been associated with both the word city walls 「城」 and the meaning to surround, to enclose (concretely realised as the word 「圍」) for a very long time, with the only clear difference being whether it has a direct sense of surround (e.g. 囿) or a direct sense of city (e.g. 邑). Once we have a dictionary like 《說文》


  囗，回 (/*[ɢ]ʷˤəj/) 也。象回帀之形。


also directly making a etymological connection between 「囗」 and 「回」, then we have a deduced assumption of what kind of word 「囗」 may have represented, if it ever existed independently and was not referring to 「丁」 or 「城」.



Characters' original forms that have no independent usage may not have the same explanation behind them, with conclusions being drawn from educated guesswork. Check out 《說文新證》's entries for 「夊」 and 「夅」.