Guest #3...
There will be some tonal differences, and yeah, you pretty much got it... the EL34's have a softer vacuum than the 6550 and a different internal structure (pentode vs beam-power tube). The EL34's will distort earlier although you would really have to have some way to A-B the differences to notice it all that much.
Guest #2 brings up an important point. If you put EL34's in your amp without this pin connection, you won't hurt the amp or the tubes... but you also won't get much sound out of it. It should be a simple modification... just a straight piece of wire, but since these amps are pretty much handmade, you might run into some major surgery if the extra pins were used as a tie point for circuit components... if the pin is unused, not a problem. And the mod will not prevent the swapping back of the 6550's at a later time.
However, the bias circuit might need to be adjusted to provide the correct bias range for each tube type.
And for additional research... all of this is discussed in Aspen's Tube Amp Book... look for the Marshall 6550 to EL34 conversion modification... and most of that would also apply for your Sunn.... although not exactly due to different circuit values.