IMO the increased bulk when in storage is well worth it. I'd call this a very minor problem compared to the benefits.
The Nikon grips I've had over the years, for the D7000, D610, D750, and D500, have all been the type with the electrical connection on the bottom on the camera. It's interesting that I acquired all these grips, except the MB-D11 for the D7000, for free under various sales promotions. I think Nikon has been too optimistic for a long time about how many of their overpriced grips would sell for full price.
I don't see how I would store an L-shaped grip in my camera backpack so that it's protected and doesn't hit anything, and where the space is used efficiently. Also it looks like the part that goes inside the camera's battery chamber could be soiled easily. But I have never used this type of a grip (all the ones that I have used have been with flat top).
From what I understand having spoken to local camera stores, the Nikon battery grips that provide functional enhancement (i.e. fps boost, such as the one for the D700/D300) have sold well but the ones that are just extra battery holders with controls but with no performance benefits have not sold as well. However, in the field I see many using one (many originals too), and many who aren't using one. It's a personal preference.
I'm pretty sure that Nikon know that many users of their cameras buy cheap knock-off grips but it's also possible that the decision not to include pins is partly because they are not interested in facilitating the knock-off grip business (but it also can lead to a simpler design for the camera, and thus lower costs and easier repair, as there are fewer connectors, wires and circuits).
Anyway, we don't have any direct influence on what features and accessories Nikon decide to offer for each of their cameras. What we can decide is which cameras and accessories we buy, based on their fitness to task and price. There is a lot of variety on the market and I am sure each of us can find suitable tools for our needs.