IIRC there was a bug in Vanilla SH3 with the 2nd Flotilla transfering to Brest.
11 years ago - playing Vanilla - I found the port at the correct location:
https://en.wikipedia.org/wiki/Brest,_France
You may want to check the (C:\GAMES\)Ubisoft\SilentHunterIII\data\Cfg\flotil la.cfg and scroll down to the 2nd Flotilla/Wilhelmshaven
Make sure the date for the location shows 09 1940.
Flotilla1=903
TO1=941
NbStartingDate1=6
NbDate1=6
Emblem1=data/Emblems/SubEmblems/Flotillas/2nd flotilla.tga
NbBases1=2
Base1_0=752;Wilhelmshaven
Date1_0_0=1939
Month1_0_0=8
Date1_0_1=1940
Month1_0_1=8
DeparturePointLong1_0=976375.000000
DeparturePointLat1_0=6422169.000000
Heading1_0=97.1805
Base1_1=753;Lorient
Date1_1_0=1940
Month1_1_0=9
(my CFG shows Lorient, just because the 2nd Flotilla wasn't transfered to Brest but Lorient; this was addressed with GWX and other mods)
Now check your (C:\GAMES\)Ubisoft\SilentHunterIII\data\Campaigns\ Campaign\messages_en.txt - assuming you run the english language version.
Find the radio message concerning the transfer to Brest and edit it accordingly to match 'September 1940' (late August).
(my modded version reads: 19400828 1200 19400829 1200 1 100 20 A new submarine base is available for operations in Brest.|Bdu)
All modifications to the data only while in your homeport! (SIC!)
You may have to replay the last sortie from Wilhelmshaven and delete all later savegames.
edit: rethinking your problem, the radio message was triggered early. Just sail to Brest and the port should be there - depending on the original Vanilla flotilla.cfg date (should read 08/28/1940, but yours may be different).
Installing i.e. GWX would solve the problem too. I guess you have your reasons for playing Vanilla?