I tried it both in Mesen and VBA-M, and the slowdown with several objects on screen (even if just bullets) is present in both. With ~4 bullets on screen everything starts to slow down -- not any extreme slowdown, but noticeable. I noticed it in a bunch of different rooms, not just "special rooms".
Yeah, the browser latency might be system dependent---just thought I'd point it out as (for me) it ran way better in a local emulator and the browser performance was not indicative of the game's quality.