My only theory is far-fetched. But it would be exciting.
What if the two men in tights were members of another Organization?
Let's say the BO is truly looking for immortality. And let's say there is another organization rivaling them in the hunt for the "fountain of youth" (I will call them the White Organization, or the WO, for a lack of a better name). Now, Gin is obviously very intent on finding Shiho, and no matter how much he probably hates the WO for being his rival, he probably mentioned Shiho and his search for her. The WO probably found out what she looked like either through research or through some other BO member. Accidentally, a WO noticed a shape in Agasa's glasses in the video. They blew up the picture and there was chibi Shiho's face, staring straight at them. The WO member (I'm assuming he or she is of a high rank) probably theorized that the BO's Shiho had managed to find the immortality drug and shrink herself to escape the BO's clutches. Now the WO member is smart and decides to kill two birds with one stone. The member thinks that if they manage to capture Shiho, they'll get the immortality drug and have the upper hand over the BO in terms of research, finance, info, etc. So the member orders two lowly members to kidnap her and bring her back to HQ. But, of course, they take the wrong girl.
If this theory is true, then it'll bring forth an entirely new story plot and way of thinking.
I'm pretty sure this is all not going to happen.
I bet it'll be better in a fanfic, but I just wanted to put it out there, just in case.