Альтернатива Base R с использованием by
do.call(rbind, by(df, df$Name, FUN = function(x)
c(Count = length(x$Value), TRUEs = sum(x$Value == TRUE))))
# Count TRUEs
#a 3 2
#b 1 0
#c 1 1
Или с использованием tapply
do.call(rbind, with(df, tapply(Value, Name, FUN = function(x)
c(Count = length(x), TRUEs = sum(x == TRUE)))))