Exactly. With no reserves the market rate will be exactly that, not an arbitrary value decided by BW based on what they would like to receive, loosely informed by conditions during an economic (and boating) boom. The current system of reserve prices is preventing the market deciding a value for the moorings.
It may be that there are a few moorings that are genuinely unwanted but it seems likely that most failed auctions would succeed if the prices were allowed to fall below reserve. This would at least secure some revenue for BW, rather than none, and deflect the criticism involved in setting reserve prices, let alone the criticism that administering a system of fixed prices or a waiting list would result in. Conversely, the system would still allow prices to rise in periods of high demand (as before the recent economic downturn), to BW's benefit, and therefore hopefully to the benefit of the waterways. If an auction failed a couple of times, BW would have evidence that a particular mooring was currently unwanted and it could be removed, if there really was an individual cost associated with maintaining it.
The only obvious way a genuine open auction system could be manipulated would be by agreements among the potential buyers to keep bids low and, presumably, allocate moorings between themselves on some other basis than cost. Given the level of disagreement among even the sample of boaters on here, I think BW would be safe from that eventuality