I would recommend you to use the whole information (to include data from night hours) : firstly adjust your data for the intra-day periodicity with a deterministic function, secondly you can fit your arima on the periodicity adjusted series. You'll be able to recover the original non-adjusted series by post-multiplying your mean estimates by the deterministic factor.
See also here : Is that a good way to work with the ARMA model?Is that a good way to work with the ARMA model?
