I don't think this puts Amendola's roster spot in any jeopardy; who are they going to replace him with? No one left in free agency is as good as he is, and worse players like Mohamed Sanu are getting paid substantially more money in free agency than he's due next year, and they're all getting long-term deals.
Hogan plays in the slot and outside, while Amendola plays almost exclusively in the slot. Like you said, given how injury-prone Amendola and Edelman are and how important they are to the offense, having versatile insurance for them who can also play alongside them is really important. Hogan's, at worst, no less capable than Sanu and is likely to come much cheaper.