The Red Devils are understood to be close to finalising a transfer for the 24-year-old, who was made the club's top target by manager Jose Mourinho after an early end to their pursuit of Antoine Griezmann.
Del Bosque admits that it will be disappointing to see Morata depart the European champions, but it will not affect his place in the national side ahead of next year's World Cup finals.
"What is good for him is mainly that he plays but I think he is doing very well at Real Madrid," he told reporters. "It is a shame if he leaves.
"But I have always said that it is an enrichment factor for our football that our players have been able to go abroad and have been able to play. It will not be a problem for the Spanish team."
Morata, who netted 20 goals in 42 outings last season, is said to have ended his honeymoon early in order to push through a move.