From the security point of view the most obvious difference to me is that Nitrokey contains a secure element while Secalot doesn't. (Secalot contains a microprocessor with cryptographic acceleration but don't confuse this with a secure element.) Secure elements are secure key stores which protect against extraction of cryptographic keys by malware and by physical attackers.
Also Secalot seems to be a small project while Nitrokey is a (small) company, which might influence quality of security and maintenance too.
Disclaimer: I'm with Nitrokey UG.
