There are a ton of sites out there to help book hotel rooms and to aggregate all the different sites to book hotel rooms. These companies make enough money to buy ads on TV, so I won't name them here. I normally poke around 3 or 4 of these as part of planning any trip.
I am now starting some very long term planning for a 6 week South Pacific trip, which includes undertstanding what hotels costs on some very small islands. I have paper guidebooks and I've been looking online. But I come across anomalies. For example, a place which has only 9 hotels listed on the sites I use, and prices range from $1000/night down to $200/night, then when I read the reviews on that cheapest one people are saying "it's nothing special, there are 5 or 6 places just like it here for half the price". Well, not on this site there aren't!
My guess is that many of these places don't have web sites, or don't have online booking, and therefore aren't getting into the aggregators. For some islands I have found local tourism boards with lists of "pensions" and such, typically cheaper than what I can find on the aggregators.
But how can I know? I don't want to assume that popular web sites represent reality, and choose only from places listed there. But I don't want to invest 10-20 hours of research per island only to discover the aggregators had everything. How can I know where the coverage is good and where it isn't, what kinds of hotels are more or less likely to be listed at expedia, trivago, booking, hotels, tripadvisor, and the like? (For example, I don't want to stay at a hostel, so I don't mind if they're not included in online sites.) Are there sites like wikitravel that list places without much of an internet presence? I'm starting my research over a year before the trip, but wading through hotel pages is not the fun part of the planning so tell me how the smart people do it.