I was able to use layout(annotations()) scheme not on the subplot() but on the plot_ly objects themselves. This gives a slightly better placement for dynamic visualization. So to rework @d-roy's answer:
p <- subplot(
plot_ly(economics, x = date, y = uempmed) %>%
layout(annotations = list(x = 0.2 , y = 1.05, text = "AA", showarrow = F,
xref='paper', yref='paper'),
showlegend = FALSE),
plot_ly(economics, x = date, y = unemploy) %>%
layout(annotations = list(x = 0.2 , y = 1.05, text = "AA", showarrow = F,
xref='paper', yref='paper'),
showlegend = FALSE),showlegend = FALSE))`.
Please note that in this case coordinates of the annotations are the same for each annotation because they are referring to each subplot and not the combined plot as a whole.