From Paradox's FAQ on the matter:
"What will this mean for Paradox and HBS?
Harebrained Schemes will continue to operate with its own internal management and creative teams, designing and developing the games that have earned them their outstanding reputation. HBS and Paradox have a shared vision for where to take narrative rich tactical games. Of course each title will be greenlit via Paradox's publishing process. HBS will continue to have the freedom to creative direct our games and build our player experiences.
In their new role as a division of Paradox Interactive, Harebrained Schemes will gain access to an expert publisher with a strong reputation and a global audience. Paradox will handle finances, marketing, PR, and distribution, and leave the development to HBS. Paradox is bringing HBS on board because they like what the studio is doing, so nobody wants to change that. Fans of Harebrained Schemes can continue to count on the community involvement and visibility that the studio has always provided."
Whether or not you trust Paradox's words on the matter is up to you, I suppose. But I trust HBS, so I'm going to reserve judgement.