... are you talking about a single, numbered folder under the "SaveGames" folder is that large after one patrol? That is rather large. If you are talking about the size of your My Documents \ SH4 folder, then that might not be considered large...
Just to be certain:
Notice the circled "Save replay" box that is empty. NOT saving the replay. The arrows are pointing to an old save of mine that has playback with it, the little movie camera in the right column. The "flag" icon designates it as a Single Mission (Quick Mission in Stock). The little "TestSaveOfATest" there (not "Saved" yet) is from me departing Midway in June 1942, and traveling out about 10 minutes. File size for it (the "00000007" folder in my case) is 780kb - kilobytes. My SingleMission save with the replay, which is maybe 4 minutes total ("00000006" folder) is 2.83MB, megabytes. The folders are not always in numerical order either. If you delete a Save, the game might re-use that particular folder number, which is the case with my Save folder structure in Windows versus what the game has in its list. Check the time stamps of your Save folders.