It has nothing to do with the Packers game since the team had 400 + yards passing 3 TDs and no interceptions, but there is a long term issue of the team not having a traditional deep threat at the wide receiver spot, at least no one who's established himself as such. Boldin, Manningham, and Crabtree are similar in the sense that their basic game is to be "possession" guys. It didn't affect the 49'ers against the Packers because the Packer defense was focused on stopping the read option. To do that, they basically gave up some pass rush and some coverage in exchange for having someone on the Packer side of the line of scrimmage who stayed to keep containment on the quarterback. As a result, Boldin had time to get open often well downfield and CK got more time to run around behind the line of scrimmage to give Boldin the time to do it, so long as he didn't try to head up field.
There will be games this year when the 49er's offense will need to break a wideout deep and stretch the field by actually having the ball caught once or more times during the game. This wasn't that game.
I like Williams more as a YAC type receiver than as the guy who catches the 45 yard bomb. He's not blazing fast (won't seem to outrun the ball) and he's small (he won't be physically superior to the cornerback), so he needs to be open by a lot and the ball needs to be out front. The save of the low pass he made in the Packers game was probably more the sort of play I'd expect him to make on a regular basis than the jump ball that resulted from the underthrow. Larry Fitzgerald or Calvin Johnson might have caught that ball, but Williams normally wouldn't.
The Seahawks game should be interesting. It was Ck's one game where the other team appeared to get in his head. I don't, however, think of it as the game where the need for a "stretch the d" wide receiver is going to be the big test. I see it more as a test of the progress the QB has made in a year.