The more I read about the Hadith's on Khawarij, I felt they are similar to Munafiqs. Is there any difference?
A quick answer is:
Munafiqالمنافق (plural Munafiqeen المنافقين or Munafiqoon المنافقون) applies for any person who is seemingly a Muslim, but in his heart he isn't, there were some at the time of the Prophet () as the Quran describes, a major part of surat at-Tawbah (9) is addressing this topic, read for example (9:67-108). And they might be existing at any time.
The Khawarij or Kharijite الخوارج historically is the first sect who created a big split of the Ummah after the first fitna (37 a.H. after the battle of Siffin موقعة صفين) they were described in ahadith such as:
"There will appear in it (i.e, Iraq) some people who will recite the Qur'an but it will not go beyond their throats, and they will go out from (leave) Islam as an arrow darts through the game's body.' " (sahih al-Bukahri)
Read also in wikipedia:
The Khawarij initially were members of the "Party of Ali". They later rejected his leadership after he agreed to arbitration with Muawiyah rather than combat to decide the succession to the Caliphate following the Battle of Siffin. ...
This original group of Khawarij and their offspring and followers has been fought by Muslim authorities until around 130 a.H. note that many of them established in what is now known as Morocco and were for a long time predominant there.
Note that the Arabic verb خرج means leave/go out etc., so one could call anybody who left the jama'a (or majority) of Muslims a Kharijite or Khariji or among the Khawarij.
Therefore from time to time contemporary scholars call some of the "extremists" Khawarij for example ISIS and al-Qaeda have been declared as khawarij by some scholars.