Well, it depends on exactly what you mean by side-effects.
First, obviously you have unsafePerformIO, so that everything can have side-effects.
Second, you have side-effects like using memory or using the CPU. You are not supposed to worry about those. Though a more serious side effect you do have to worry about is non-termination. Haskell doesn't track that in its type system.
You are right that the way input/output is handled can be described not as _side-effects_ but as _effects_ of interpreting values of the IO datatype.
First, obviously you have unsafePerformIO, so that everything can have side-effects.
Second, you have side-effects like using memory or using the CPU. You are not supposed to worry about those. Though a more serious side effect you do have to worry about is non-termination. Haskell doesn't track that in its type system.
You are right that the way input/output is handled can be described not as _side-effects_ but as _effects_ of interpreting values of the IO datatype.