Even with a long reach excavator, you will definitely want to pump out the water, so that the operator can see what he is doing and will be able to clean it out completely, with the water in it he will get a portion of the muck out and the rest will be stirred up into a silty liquid that you will never be able to get anywhere near all of it out of your pond. jmo
And, make sure to offer the operator of the equipment a big old plate of BBQ ribs or something,, he will do a much better and faster job for you, dont ask me how I know,, you might offer him a beer or two about quitting time, most operators like that!