Over the years, June 1 has always been considered a notable date on the NFL calendar. For many years it acted as a sort of second wave of free agency, as veterans were released after the start of June in order to split up the cap hit over two years instead of one.
When a player signs a contract, any signing bonus (paid out immediately) is prorated for cap accounting over the length of the contract, up to five years. If a player is released before the end of that contract, the remainder of the cap hit is accelerated to the current season when done before June 1. However, in the past, if a team waited until June, the player's cap hit in the current year would be what it was supposed to be, and then the rest of the hit rolls into the following year's salary cap.
Plenty of great players have found themselves on the short end of the stick when June rolls around. The most notable 49ers player to get released in June would have to be Jerry Rice. Following the 2000 season, the 49ers found themselves in what had become a recurring theme of salary cap trouble.
While the 49ers had wanted Rice to stick around the rest of his career, they reached a point where that situation was simply untenable. And so, when June rolled around in 2001, he was given his release and quickly signed with the Oakland Raiders. This was not a surprise, as it was expected during the previous season, but due to the mechanics of the CBA, the 49ers had to wait until June to make the move.
That changed when the NFL and NFLPA agreed on a new CBA back in 2006. The 2006 CBA allowed teams to release up to two players before June 2, but designate them as post June 1 roster cuts. The cap savings did not impact the roster until June, but the player was a free agent as soon as the release happened. Examples of this in 2013 include Michael Huff, Ryan Fitzpatrick and Karlos Dansby, among others.
The 49ers could decide to release veterans between now and the start of the season, but they are not in a position where it is absolutely necessary. The team currently has a little over $2.6 million in cap space. Additionally, they've already re-worked some veteran deals, likely decreasing the odds those players would be released. That is enough to get their remaining two rookies (Eric Reid, Corey Lemonier) locked up, and potentially even add a wide receiver if they want to bring in some competition.