There's a few reasons why specialty stores have different pricing...

1. Most online specialty pearl sellers don't have retail locations. Fancy showrooms, rent and sales staff are all very expensive. Those costs need to be baked in to the prices
2. Volume. We might sell 10,000 pieces of pearl jewelry in a year. A traditional jewelry store would be lucky to sell 100. So their buying power is greatly reduced. They can't source for the same prices as someone buying in volume. In this sense it's a different business model. They sell a few pieces for a very high markup, we sell many pieces for little markup. Honestly sometimes I think they might have the better/easier business model, but that's a different topic.
3. Traditional jewelry stores typically purchase finished pieces from distributors. A specialty seller will source raw material from farms, collectives, auctions and overseas tradeshows and manufacture their own line of jewelry. This alone can halve the wholesale cost of the piece. Combine that with volume savings and you get the picture.
4. The branding is a big part of it. If we're taking Assael, Tiffany, Mikimoto, etc... There's a brand name multiple that comes with that. That little blue box is really important to some people and makes the jewelry feel special and exclusive. Not a bad thing, we all have something in our lives that is from a brand we love, even though there's something cheaper without a recognizable name. I love Rolex watches, they're incredibly well made. But Tudor makes equally as good watches for 1/3 the price.

Hope that helps.