Is IDS Center (3, 6) or (1, 1, 1, 6)?
My sense is that (1, 1, 1, 6) would have been preferred last century, but with acronyms increasingly used in everyday life, (3, 6) would now be acceptable.
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I would clue it as (3,6). My (albeit limited) experience with cryptics tells me that typically only spaces are considered in an enumeration - other punctuation is indicated. Also, Wikipedia says
An acronym is a word...
Your sense is correct, at least as far as most British crosswords. For example, The Guardian switched over in 2012 as announced here.