His entire (not quite) 100-day protest was based on the fact that Nintendo had yet to respond to his application for a Nintendo DS SDK, so official communication from the company is, in one sense, vindication for Pelloni. But in another, more accurate sense, it's a rejection letter.
The text of the letter offers clues as to why Pelloni was not approved: Nintendo expects "secure business facilities, sufficient equipment and staffing, financial stability and other attributes that would distinguish the developer." We assume that a sealed office that you pretend is an alien spaceship does not constitute "secure business facilities."
Even more telling is the statement that Nintendo "provides Authorized Developers with highly confidential information" and thus "exercises a very high level of discretion" when choosing to whom it grants SDK access. If he really has heard back from Nintendo (and we must express a modicum of doubt in regard to anything Bob's Game-related), then Bob's constant blogging of his own wait for approval seemingly ruined his chances of receiving that approval.