Yes, AT5 files are in general much bigger than the old LCM, but they do contain much more information, and also the option of holding raster data which is much, much bigger than vector data.
I wouldn't worry too much about AT5 map size. SD cards a big and cheap now, so there are no worries there, and the units will load data as required.
As far as which AT5 format is best, this is really personal preference. Vector maps (contours, isobaths etc) and much quicker to generate and take up less room on disk, and it is also easier to combine multiple vector maps on the unit by simply storing each AT5 file in a separate directory or using the Project Based Naming option to give each AT5 map a separate filename, and storing all of these files on the same SD card.