The gemara says that they would make special kevarim inside the me'arah especially designed for nefalim. This would indicate that there is in fact a mitzvah to bury a neifel.
The Rama in hilchos yom tov (526:10) writes that one is not allowed to bury a neifel on yom tov, rather he should be buried the next day. The source is from the Hagahos Maiomonies who holds that there is no mitzvah to bury a neifel. However, the Magen Avrohom (20) says that in his opinion there is a mitzvah to bury a neifel. The Hagahos Maimonies cites the gemara in pesachim 9a which implies that there was a pit that was designated to throw nefalim into, implying that there isn't any mitzvah of kevurah. The Gr"a also takes this approach, that the fact that they were thrown into a bor indicates that there isn't a mitzvah of kevurah. But, the M.A. disagrees and holds that being thrown into a bor would qualify as a kevurah. Furthermore, the M.A. cites a proof from the Toras Kohanim which says that a Kohen cannot be metamei for his son or daughter that is a neifel - this implies that there is a mitzvah of kevura because if there wouldn't be a mitzvah of kevura it would be obvious that a kohen can't be meta'mei since he can only make himself ta'mei for the purpose of kevurah. Finally, he cites our gemara which says that they would make graves for nefalim, implying that there is a mitzvah of kevurah. The M.A. ends by saying that the gemara in Nidah implies that not only would there be a mitzvas kevurah for a neifel, but there would even be a la'av of ba'al talin. On this last point, the Nodeh B'Yehuda (o.c. kama end of 16) says that he doesn't understand where the M.A. is drawing his proof from that there is a violation of ba'al talin. The N.B. argues that m'svara the la'av of ba'al talin (not leaving the deceased over night) is a din in kavod ha'meis which would not apply to a neifel. The machatzis Hashekel tries to justify the proof of the M.A. that there would be a la'av of ba'al talin, from Tosafos in Nidah 57 who says that the kusim would temporarily bury the neifel with the intent of moving them later. If they were going to move them later, why bury them temporarily? This implies that there would be a violation of ba'al talin that would compel one to bury the neifel temporarily.
It seems to me that Tosafos in Pesachim 9a also holds that there is a mitzvah to bury a neifel. Tosafos writes that the kohein who leaned over to check if there was a neifel in the pit was a fool. why? Because even if it was his own child, a kohein can only make himself ta'mei for a bar kayama, not a neifel. Tosafos continues - ועוד דכאן לא היה לצורך המת. Tosafos says that the kohen couldn't make himself ta'mei because it wasn't a need of the meis. This implies that if it were for the purpose of burying the meis he would be able to make himself ta'mei, presumably because there would be a mitzvah of kevurah (proof to magen avrohom). But, perhaps Tosafos means to say that a neifel is always considered not l'tzorech of the meis since there isn't any mitzvah of kevurah (like the hagahos maimonies).