Indeed there are! As far as I can gather from the Net, Castro's boys were less Cromwellian with organs than your typical post-V2 American parish. This is a recent installation in Havana's oldest church, claiming to be the first 2-manual instrument in Cuba (which it isn't) Skinner Op. 584 is in Holy Trinity Episcopal Cathedral, but is apparently not in a playable state. Aeolian Op. 1755 is in the Dupont Mansion in Varadero, also not playable.
If you're a member of the Facebook Organists group, I believe there was a discussion in the past few months, because someone "schooled me" on an organ I thought I knew in Havana!
To participate in the discussions on Catholic church music, sign in or register as a forum member, The forum is a project of the Church Music Association of America.