Yahweh came, and stood, and called as at other times, Samuel, Samuel. Then Samuel said, Speak; for your servant hears.
This appearance of the Lord to Samuel had nothing whatever to do with Samuel's sleeping where the ark of the covenant was kept in the Holy of Holies, for it is NOT true that Samuel slept there.  God was, in no sense restricted to the ark of the covenant as a place where he would speak to men.  Like other great Christophanies of the O.T., the location of the person visited by the Lord had nothing to do with it.  Furthermore, the fact of any particular name of God being used in this passage is likewise of no significance whatever.  Literally, dozens of names of God appear in the O.T., and they are often used interchangeably, sometimes as many as five different names of God being used in a single passage  (Genesis 49:23). It would appear from this that the appearance of the Lord here was similar to that of his appearance to Joshua  (Joshua 5:13-15).