The answer is, like usual, "it depends".
What the FULL_ES2 emulation does is it allows the user code to render from CPU-side memory arrays. When you do glDrawArrays/Elements while having such arrays bound, the emulation will create its own VBOs under the hood, upload the CPU-side data to the VBO (with glBufferData/glBufferSubData), and then render that.
As a result, this means that every draw call from CPU memory results in a full reupload of that memory to GPU before drawing, and that is the performance hit.
If you are rendering static geometry that could only be updated once and then rendered multiple times, then the emulation path cannot know and take advantage of that, and you could do less work by manual VBO management. On the other hand, if you are rendering dynamic geometry that needs to be uploaded to GPU each frame anyways, then chances are that the difference will be very small.
Generally we would definitely recommend avoiding FULL_ES2 whenever possible. One way to estimate the impact before having written the port is to use a browser profiler to measure how much time is being spent in the GL context bufferData & bufferSubData functions - those should be where the most of the added cost comes from, assuming that you could avoid redundant buffer uploads if you used VBOs manually in the code.
Jukka