In most cases, these recipes specify whether to use bone-in or boneless chicken thighs in their preparation. In some cases, the reason for doing so is clear – for example, in recipes in which the final product is small, fried, boneless pieces, there is little reason to start with a whole bone-in thigh. In other cases, the recipe specifies starting with a bone-in piece only to discard the skin and bones at some later step in the recipe. While you could simply skip straight to the boneless piece, in many such cases, the bones, skin, fat, and gelatine of the whole piece contribute to the flavor and texture of the final dish. This is particularly accurate when using the thighs to fortify stocks.
The same holds true for some of the baked and roasted dishes. While a boneless piece can be substituted when fat content is a concern, the final product may not have the same flavor and texture.
Buying bone-in chicken thighs and deboning them when called for has the added benefit of leaving you with chicken skin, fat, and bones, all of which can be utilized to make sauces, stocks, and cooking mediums such as flavorful schmaltz (chicken fat rendered with onions). I keep skin, bones, and trim in the freezer for future use.