How would you remove games? ULaunchELF -> HDDManager and delete whichever game partition? I'm assuming that would cause fragmentation eventually though. WinHIIP throw a memory error with 2TB drives, otherwise that would be easier for removal I'd assume, but it might just do the same thing.
To delete, you can use HDDManager and delete the partitions like you described. Or you can also use OPL, turn on the Enable Write Operations setting, and then use the on-screen buttons in the games list menu to delete the selected game.
As for Winhiip, it only works on drives 1TB or smaller. But even when it works, it has many issues because it is so outdated. If you should happen to have games that are very similarly named (e.g. multi-disc games), Winhiip can be extremely destructive when using its "defragmentation" or "repair" option. The reason why is that it uses the game's title to rename partitions. So when you have many titles that are similarly named, what can happen is that they are all viewed as the same game (because partition names only allow so many characters, and the partitions are named after the game titles). So all these unique games will collide, and you may very well end up with all the games overwritting each other into a single game. (Winhiip does not make use of game IDs to create unique partition names, contrary to the official Sony SDK specifications. The latest HDLDUMP used in HDLBATCH, however, does use the game IDs in the partition names, resolving the issue above.)
Fragmentation is really only an issue for playing via the USB port (using an external HDD) because the bandwidth is extremely low. So a fragmented external HDD would make any bandwidth-related issues even worse. On the internal disc, games are installed using a parent partition, and (if necessary) children partitions. Ideally, these parent-children partitions would be next to each other. However, even if they are not, it really is not an issue because the partitions themselves are allocated in such a way that you have minimal partitions, each of maximal size. So unlike a fragmented file that might be split all over a platter, or multiple platters, on an HDD, the partitions are fairly large and you usually only see a handful of them, and only for very large games. And with HDD speeds being vastly faster than the optical drive, fragmented partitions really do not pose any issue.