There was definitely some truth in that. When eBooks were relatively new there was a widespread trope that they "should" be a lot cheaper than physical books because they didn't have all the printing/distribution/return/etc. costs associated with dead tree versions. In fact, these costs were pretty trivial (maybe $2/copy as I recall).
And pre-Amazon, in 1990s dollars, B&N 25% discounts on bestsellers was a big deal when non-discounted $25 hardcovers was the norm. (Mainstream eBooks came a bit later of course but the basic point that the cost of providing a physical book was a lot less of the cover price than most people assumed it was.)
The weird part about that is that, back in the 80s-90s, book prices took a big hike and the publishers blamed paper prices.
Their reasoning is amazingly flexible.
Also note that all of the non-printing, etc., costs are one time affairs. Except for the distribution channels, which take ~50% of the cover price (and which don't apply to e-books).
I heard a different explanation in the early days of ebooks: that publishers were afraid ebook pricing and lack of physicality would diminish the perceived value of print books. This from a few in the print publishing industry, but I don't know how widespread it was or is.