Hi Aloha
The problem is two-fold. Generally the iPad's output through the headphone socket is plenty loud, and while it's probably possible to buy headphones with built in amplification, you'd run into distortion problems, especially on spoken word material, which I presume as scientific films the videos mainly are.
The main issue is with the videos. If the sound has been mixed too low in them originally, then short of demuxing the video and audio in a video editor, normalizing the audio and then recombining the two streams it's hard to see what can be done. The iPad can only work with what's in the original video, after all.
Sorry couldn't be of more help - it might be a case that the offending videos will have to reserved for home watching, sadly.