The oceans are deep, wide and dark (okay, not so much in the Aquanox games), but it's probably not that easy to find a ship and get it back in one piece (also considering Flint got a better ship later on). Even if he wanted to, there are probably hundreds of thousands ships roaming the oceans.
It's been an interesting plot twist to explain starting out in a weak ship again, but I never really liked this explanation. It just sounds too weird. Why/how did he take the ship AI with him (considering he didn't want to give up the ship)? Aren't there any security measurements keeping someone from just hopping into someone else's ship? It's been the most modern fighter sub in whole Aqua and someone unable to pilot it properly has been able to hop in and hijack it? It's no simple jeep, it's a high tech ship with an AI and stuff.
In the end, he isn't happy about losing the ship (more likely due to having to start from scratch once again; not due to losing the specific ship), but due to the fact he's able to gain access to more advanced ships later on, I wouldn't expect him to specifically hunt Freeman down. If he runs into him, why not, but specifically looking for him? I don't think so. This most likely doesn't fit his personality as well. He's a mercenary, but the whole plot around Hong Long in the first game suggests that he's more than likely to grant mercy and let someone get away if there's no money or shooting at him involved.