In 2015-2016, the New Glenn design was expected to use a single BE-4 methane-LOX engine on the second stage (about 2400kN thrust), and a single BE-3 (the same as the suborbital New Shepard's single engine, and likely in the 500-600kN range for the upper stage version) on an optional third stage. There wasn't any need for an engine in between the power of the BE-3 and BE-4, so Blue Origin didn't develop one.
By 2018, the design had changed, and the second stage apparently no longer needed the thrust of a BE-4; instead, a pair of BE-3Us would be used, producing together about 1400kN thrust. The BE-3U is an expander-cycle version of the BE-3, and presumably it could be developed much more quickly and cheaply than a new engine optimized for the New Glenn second stage.
If and when the New Glenn gets ordered in large numbers, Blue Origin might find it worthwhile to design a single cheap engine for the second stage, but that kind of thing hardly ever happens in rocket development -- the production runs are so small that the effective cost of each successive unit (taking into account the development cost amortized over the number of units) drops very rapidly.
As a rule of thumb, research and development costs for aerospace hardware run around 10x as much as the production of the first unit; the first unit costs around 5x as much as the 1000th unit.
Assuming that the hypothetical right-sized engine costs 1.5x as much as a BE-3U, and using the above rule of thumb for R&D cost, using the two smaller engines is cheaper through the first 30 flights, at which point the savings on a single big engine pay off the cost of R&D.
At this point, however, Blue Origin's biggest concern is getting the rocket flying as soon as possible so they can start competing for customers with SpaceX. Developing a new engine is a long process that would set New Glenn back by years. The incremental cost of expended engines is a small concern, and Bezos's greatest successes to date have been achieved by throwing away vast amounts of investor money in order to strangle the competition.