Northern Ireland Protestants voiced outrage at hopes for Irish reunification publicly expressed by US Undersecretary of State William P. Clark Jr. In a letter delivered by Mr. Clark to Irish Republic Prime Minister Garret FitzGerald, President Reagan last week endorsed joint efforts by the British and Irish governments to resolve the sectarian conflict in Northern Ireland. In a television interview given before leaving Dublin, Mr. Clark said: ''Certainly the hope and prayer of all Americans is that this will ultimately lead to unification.''
When Ireland was partitioned in 1920, Northern Ireland remained part of Britain. Conflict between the Protestant majority and Roman Catholic minority there has flared into violence in the last 12 years, claiming more than 2,000 lives. Mr. Clark's remarks angered Protestant leaders because they appeared to be in line with the wishes of Mr. FitzGerald for the ultimate reunion of Ireland. Protestant leaders oppose reunification with the largely Catholic Irish Republic, saying they would rather be independent if they could no longer be part of Britain.