I would save them as cell arrays:
Example:
data1{i} = H5D.read (data_id,'H5T_NATIVE_DOUBLE', 'H5S_ALL', 'H5S_ALL', ...
'H5P_DEFAULT');
time{i} = H5D.read(time_id,'H5T_NATIVE_DOUBLE', 'H5S_ALL', 'H5S_ALL',...
'H5P_DEFAULT');
time1lvl{i} = datestr(datevec(datenum(1993,1,1,0,0,0)+time(1)/86400));
Note the curly brackets ‘{}’ denoting cell array indexing.