Yes, and no. Minecraft works with a game loop (=ticks). What this means is that everything that has to do with the worlds runs on 1 thread. Every tick the server has to update the whole world, block placement, removal, loading chunks, lava & waterflow, locations of mobs/players etc and execute code called in bukkit plugins. You get server sided lag whenever: 'time needed to execute code for an arbitrary tick' > 'time reserved for that tick =1/20 second'.
Back to dynmap, dynmap is coded so that major parts of it run on another thread, reducing the effect on the game loop. The maps implemented in Minecraft, do run on the same thread as the game loop, and could potentially cause lag.
Back on topic, I hope that maps no longer create the massive amount of lag as they used to. You'll have to ask naith/stoux, they could potentially re-allow them.