The cost of old products has bearing on the costs of new products every single time and Nintendo will look at the 3DS just as they did when pricing every single hardware they released before.
And again, Nintendo is the business of making money.
Have you ever priced a product? Like Seriously. I didn't make that up.
I am not saying they aren't in the business of making money. In fact I clearly stated the basic manner in which they determine the amount of money they want to make on a product.
From an accounting side they use the BOM & COGS(cost of goods sold) to determine a price range based on GMROI( Gross Margin Return on Investment ). Sometimes marketing costs and other R&D costs are rolled in this pricing, sometimes not.
That range is then handed off to marketing people who in turn do market research to best understand what price they feel the market can bear.
So yeah, I guess in a little way, Nintendo can see people still buying 3ds/2ds at a range of $79 to $199 and say yeah we can probably be at $249, but ultimately that priced is derived by many other factors with a lot more weight than just, 3ds is X so we should price new thing @ Y because it is new.
3ds and New 3ds are priced to recoup the costs associated at a specific margin while still selling as many as possible. Switch has a completely unrelated BOM and costs and will have to recoup those costs and the pricing will be more determined by this than anything else. If Nintendo cocked up somehow and spent too much, you can damn well believe they'd charge $300 or more, regardless of whether they think the market could truly bear it.