Inside the bullet would definitely work for a 3rd or 4th Doctor's sonic, easier to hide in the 4th's with the longer 'magnet' end of the bullet - and if I'm not mistaken, that's the end that is arguably used more often during functionality. The 8th Doctor's, not so much, as the bullet is smooth on the flat end where the other two have a recess.
The challenge, aside from the gestures in vertical orientation, would be hiding it enough to not spoil the look but also not so deep into the 'magnet' that it interferes with sending and receiving a clear signal. From the looks of it, the other two sonic remotes have 180 degrees of clear sending/receiving area from the tip of the IR LED. I've had my 10th sonic almost vertical and still gotten it to work with the TV B Gone function. But with the LED embedded into the 'magnet', it could limit the range to anywhere from 60-90 degrees depending on how deep is enough to hide it well, and that's if the proper end of the emitter is facing the device dead on.
Long and short of it, River Song's would be the best candidate, as even a proper laser screwdriver would have the same issue, minus the vertical orientation, with the LED's being recessed a few mm from the opening of each extension of the emitter head.
While we're at it, is anyone else entertaining the idea of a vortex manipulator universal remote? :lol Although I jest, the functionality would not be limited to one button and motions, but have a wide range of usable buttons.
Between the 'd-pad' on the left side and the three large buttons along the top, menu navigation would be a cinch (could even have the center of the 4-way pad be a click for enter, and the button just above and to the right could be to switch between banks to channel/volume control, etc. And the possibilities in FX mode...don't get me started.