Missing indexes dmv count varies every day
Missing index info will be cleared from the view if the referenced table has changed. Added columns, new indexes would clear out this data. When you remove indexes, any missing index info for that table will also be removed. 

Index rebuilds also clears out this info, so if you are doing nightly index maintenance, this may contribute to the change in numbers. (edit: rebuilds only clear missing index info on 2012+)