ok, I found a problem, it's not with TMT but with original B&D mod actually
Rubini put ships deeper into the water, obj_Hydro\Surfaced\draught parameter was modified for each ship
unforutanately .cfg files for the ships were not corrected, so now let's take Nelson as example:
- modded .sim file says it's surfaced draught is 12,23m (original 11,035m)
- .cfg file says it's draught is 11,04
shooting magnetic torp at 12m according to information from recognition manual would be probably result in torp bouncing of rounded hull..
looks like all .cfg should be corrected to
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GWX 3.0, OLCG2, Waterstream+Exhaust Combi v2.3, Lifeboats&Debris v4, Torpedo damage v2, TMT

and a nice skin
SH3 forever

keep modding