Using timetables, retime makes this simple. It sounds like you want an average for each day only considereing the values between, say, 8am and 8pm. Create a time vector at 8am and 8pm spanning your data, and retime to that, using 'mean'. Then throw away the corresponding to 8pm to 8am.
If you don't have access to R2016b or later, you can still do this with tables. I'll assume your date variable is a datetime. Create a subset of your data using something like (8<=hour(t.Date) & hour(t.Date)< 20) to select rows of interest. Then creat a new variable in the table using the dateshift function to truncate your timestamps whole days. Then use varfun, grouping on your day variable, and compute the mean of your data variables.
