Literally taken, "es in sich haben" means there's more "in" (to) something than can be seen on first sight from an outside view or what was or would be initially expected. Or even more literally, there is more, or a different or surprising contents in something.
Dieser Schnaps hat's in sich
Dein Kaffee hat's ganz schön in sich
could refer to some more alcohol/caffeine than expected.
Das Projekt hat's in sich
would denote there are more problems/challenges than expected.
Die Matheaufgabe hat es in sich
Could be exceptionally difficult, but could also be generating exceptional new insights.
I wouldn't necessarily say the expression is meant to have a negative sense though (at least if you don't generally see the unexpected as negative) - It just says that there's more to something than what was expected at first sight or considered "normal" and to express surprise.
In your example sentence, this could either mean the welcome is considered exceptionally warm (maybe a passionate kiss?) or exceptionally repellent (grim face and no "hi"). Could be both, the expression just says it is somehow exceptional and unexpected.