Going with TWoS, you'll have a stable game, arguably even more than SH3 in that from what I gather SH5 saves are less prone to getting corrupted when saving in contact with enemy (that was my main gripe with SH3, engagements in these games last long and it is often impossible to break contact before saving). Most issues reported in TWoS bugs thread are connected to either not following install instructions or installing random mods on top of TWoS, so don't do either of these things and you don't have to worry about stability.
Bugs aside, SH5 gives you less options than SH3 in some areas (same crewmen, only type VII boat) while being more developed in others (crewmen have some personality and you can interact with them more, you can walk around the boat freely, TWoS also includes working Enigma machine and wonderful Real Navigation addon which removes GPS position marker from the map but in turn allows your navigator or yourself calculate position from the stars or land observations, which is a lot of fun and allows you to feel more like a sailor, not knowing your exact position). Graphics are obviously better in SH5, but modded SH3 also looks nice.
Since both games are old, you can easily buy both especially if you catch a Steam sale where they regularly appear for peanuts - this might be best option, just buy both and try them yourself.
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