The 49ers do both from time to time (usually both on the same play). They run something similar to what they ran in the 90s (and in fact the front isn't that different from Seattle's). As for the strong side DE, he essentially plays the role of the NT in a 4-3 under front. The other DE plays the role of the 1-gap DT in a 4-3 under front. The ROLB plays the role of the Leo, and the LOLB plays the role of the Sam.
This was actually done by the 49ers in the late 90s, and in fact they had a mix of 4-3 and 3-4 personnel (Ricky Jackson played defensive end, but he has always been a linebacker). Dana Stubblefield sometimes (though not always) was on the nose playing 2 gaps, while Bryant Young was usually an up the field 1-gap rusher. Ricky Jackson alternated played the Leo.
Of course, today's 49ers play mostly in nickle, with the two DE's playing DT, although the players are good enough to do either 1-gap or 2-gap should the need arise.
EDITED TO ADd:
In fact here is Pete Carrol chiming in on those late 90 49er defenses:
http://www.bigcatcountry.com/2013/1/...e-leo-position
"
We mixed the concepts of one-gap football and two-gap football in a very unique way in San Francisco," Carroll said. "And we played great defense. To me, that was the ultimate package, and we've been able to get back to it now. It's taken us three years, really, to get to the point where we can incorporate the ideas. So, we're doing all of the things that we liked there. I thought it was the most comprehensive package of defense that I've been around. I was not able to do that at SC. I was the defensive coordinator and putting the whole thing together at SC, but our guys just couldn't handle it. It was just too much stuff, and it was too much for the coaches. So we did variations of stuff. It worked out great, but in college, we weren't capable of doing all of that. Guys couldn't learn and couldn't teach it the way we needed to. But it made sense to Gus and all of our coaches -- the background and the principles of things -- and then we've melded it together and ended up with a pretty diverse package of defense."