Ethics of pricing
Interesting question : the practice is as old as selling, but you object to it ethically or at least raise the question of its morality. I have not considered the practice from this angle before, so appreciate your presenting it from a (to me) new perspective. Of course the question stands, and retains its ethical relevance, if just one store sets prices in this way or even thinks of doing so. So we can set aside the quantification, 'almost all'. This is no point against you.
You use a variety of terms : 'manipulation', 'lying', 'dishonesty' - and implicitly 'deception' when you talk of getting people to believe that they are getting a better deal than they actually are.
I am going to use this term because the activities you attribute to shops all appear to be forms of deception.
Let's look for some help from the late Bernard Williams who detects two elements in deception, or two kinds of deception :
When deceiving a person is wrong, what makes it so? In the
middle of Truth and Truthfulness, Bernard Williams answers
this question twice.' He argues that the wrong in deception
should be understood in terms of a deceiver breaching a trust with
the deceived. And he argues that it should be understood in terms
of the deceiver manipulating the deceived. (Alan Strudler, 'Deception Unraveled', The Journal of Philosophy, Vol. 102, No. 9 (Sep., 2005), pp. 458-473 : 458.)
In a fuller analysis we would need to consider how the two elements or kinds of deception fit together, if indeed they do. Perhaps breach of trust is a form of manipulation, as Strudler suggests (458). But we can set this problem aside for present purposes.
Breach of trust
When one shops one reasonably expects the vendor to be reliably truthful - about the price of a product, its quality, its conditions of sale (the shop's returns policy), its functions or utility, about how to use it and so forth.
When a product has a price tag of 4.99 instead of 5.00, or 99.99 rather than 100.00, it is not immediately obvious that the vendor is committing a breach of trust. There is, indeed, perfect truthfulness about the price. This is what you will pay if you buy.
This seems more fertile territory. It's not enough to say that manipulation is a case of getting someone to do or omit doing something they would or might not
otherwise do or omit. It is this, but it's also more than this; it has to be, because this characterisation does not distinguish manipulation from coercion or persuasion.
I offer this provisional account of manipulation (not Rudinow's but triggered by his article in References) :
A manipulates S if A motivate S's behavior by playing on a cognitive defect or vulnerability of S.
This is offered only as a sufficient condition for manipulation : it is certainly not necessary and sufficient. I am not even sure that manipulation is capable of definition in terms of necessary and sufficient conditions; if may, for instance, be a Wittgensteinian family resemblance term (https://en.wikipedia.org/wiki/Family_resemblance).
But back to the shop. By pricing at 4.99 or 99.99 the shop is using a bit of highly practical and untechnical psychology. We tend, or many of us tend at least on occasion, to pay primary attention to the dollar or pound price. Dollars are much more important than cents, and pounds than pence. What catches my eye is the '4' in '4.99', not the '.99'. Equally in the case of thousands, it's the '2' in '2999' that first registers and not the trailing '9's. Shops are well aware of this cognitive defect or vulnerability and their reliance on it is a form of manipulation. By setting the price at 4.99 the vendor gets me to do something I would or might not otherwise do - buy the product when I wouldn't or might not if it were 5.00.
Joel Rudinow, 'Manipulation', Ethics, Vol. 88, No. 4 (Jul., 1978), pp. 338-347.
Alan Strudler, 'Deception Unraveled', The Journal of Philosophy, Vol. 102, No. 9 (Sep., 2005), pp. 458-473.
Bernard Williams, Truth and Truthfulness, ISBN 10: 0691102767 / ISBN 13: 9780691102764
Published by Princeton University Press, 2002.