To expand a little on Chandler's answer. Crannogmen indeed do not go much outside of their swamps (you know, they stick to Cthulhu and stuff ;) ). When you talk about Reeds and Greywater Watch, you don't picture normal castle and feudal lords. Their castle is known to move and no enemy can conquer them because Reeds and crannogmen will move through swamps and marshes and avoid the fight. So it is surely not castle like citadel with walls and Reeds don't have soldiers and shiny armors and swords.
It's been a while since I read the books (only the first three books) so someone may correct me. Howland was actually personally interested in seeing the world outside, so decided to travel around on his own and went to Harrenhall tournament, seeing Starks in person. He was the son and heir to the lord, but like I said, he's crannogman. He looked in a way that servants to some southern lords felt free to harrass him, something they wouldn't even dream to do to someone on higher feudal level. So when the Robert's rebellion came, Howland went to help the Starks in battle and is either the only one of the crannogmen or perhaps there was a handful of his men with him, but surely no armies because that is not the way of his house nor people. After this he stays in his lands and like other of his countrymen and doesn't communicate with outside world. It is unsure what crannogmen actually pay as tribute to Starks, but it is surely not soldiers nor steel, and probably no gold either. Some food, most likely.
So, when reading the book and not suspecting that Brandon may actually get to see and learn everything, it was clear from storytelling point of view that you would keep the only witness of Tower of Joy events besides Ned for sometime later in the story. He surely knows some secrets and it was interesting enough to see his children join up with Brandon, seemingly knowing or suspecting something is off with the whole story. That is something we know from the show as well and we learn from his children that Howland is alive and well.
So, short answer is: nothing happened to him, he's alive and living in his lands, not appearing because of crannogmen habits and because whatever secret he knows he won't easily let others find out.