Is the 5 speed better than the 4 speed SS? Yes and no. Both have their advantages and yes both have weaknesses too. Both are very expensive to repair and a clutch can set you back over $700 at the dealership. The SS in my car works just as advertised (bought new 3/99). Shifts when told to in SS mode and I don't worry about it. Our race car has a 5 speed and it has 176,000 in it and runs like new. Both trannys are very good on track.
The big problem with the SS has been due to the way it handles torque. This tranny is a takeoff of the Tiptronic/F1 type gearbox-which is sequential; that means it goes thru the gears one by one regardless of what you tell it. The manual is immediate in its response to a gear change. Many failures of the SS can be attributed to "neutral dump" which is a real no-no. Some have failed for other reasons. Mine just works as advertised because I have cared for it for 33K according to the manual. Our other Hondas with 5 speeds get the same TLC too.
I will strongly recommend that if you really want a 5 speed-then trade for it. Why? Simple-resale value of a car with a swap is nill compared-yes the dealers and buyers can tell from the VIN. Otherwise, keep the car you have and enjoy it. I take mine to the track for HPDE and have a blast along with taking it for trips. THe SS is simply the best touring car I have ever owned-loves to go really quick on the interstate