The reason why you are getting this warning is in the description of fun.aggregate (see ?dcast):
aggregation function needed if variables do not identify a single observation for each output cell. Defaults to length (with a message) if needed but not specified
So, an aggregation function is needed when there is more than one value for one spot in the wide dataframe.
An explanation based on your data:
When you use dcast(df, Id + Task ~ Type, value.var="Freq") you get:
Id Task A B 1 3 1 2 3 2 3 2 3 0 3 4 1 3 3 4 4 2 1 3
Which is logical because for each combination of Id, Task and Type there is only value in Freq. But when you use dcast(df, Id ~ Type, value.var="Freq") you get this (including a warning message):
Aggregation function missing: defaulting to length Id A B 1 3 2 2 2 4 2 2
Now, looking back at the top part of your data:
Id Task Type Freq 3 1 A 2 3 1 B 3 3 2 A 3 3 2 B 0
You see why this is the case. For each combination of Id and Type there are two values in Freq (for Id 3: 2 and 3 for A & 3 and 0 for Type B) while you can only put one value in this spot in the wide dataframe for each values of type. Therefore dcast wants to aggregate these values into one value. The default aggregation function is length, but you can use other aggregation functions like sum, mean, sd or a custom function by specifying them with fun.aggregate.
For example, with fun.aggregate = sum you get:
Id A B 1 3 5 3 2 4 4 6
Now there is no warning because dcast is being told what to do when there is more than one value: return the sum of the values.