Their objective this time was information. SHIELD had thousands of agents, maybe even close to ten thousand by this time, and each one had a weakness. It was all in their personnel files and waiting for the right person to exploit.
Hydra wanted the information for their own use as well as selling it to the highest bidder. Information like this would go for a few million on the black market. The trick was getting the information before SHIELD could find out what was going on.
Penetrating the base was easy and it didn't take much effort to slip past the few agents stationed to get to the central computer core. Two minutes to download the information to disc and then another minute to slip out.
The only way SHIELD would know what happened is if they actually checked to see if the personnel files had been accessed. Hydra was counting on SHIELD not to be so diligent.