A voice in a fugue may move between hands, but surely you are familiar with this from the inventions - especially the three part ones.Hand separate practice for these is completely pointless.
I agree with j_menz here. Indeed, when studying fugues I write a new score with one staff per voice (it's a good oportunity to practice the C clef also with some inner voices). On that score I mark detailed phrasings, dynamics, ornaments and, precisely, fingerings (in the inner voices you'll need some convention to distinguish which hand is playing it). I would not practice hands separately. Instead, practice each voice (with correct fingerings), as suggested by j_menz. With the middle voices you'll need to be really aware of how you pass them from one hand to the other, it must be impreceptible. You can also choose two or three voices and practice them likewise.Finally, mental practice is fundamental, you don't want to rely on muscle memory alone. Writing the separate score helps a lot in this aspect. You should understand what each voice is doing always (it is only rarely unrelated with the theme and countersubjects).Again, it is difficult, but very rewarding to dedicate yourself to these masterpieces.