No, you misunderstood that completely.
Strike craft are always good. Heavy cruisers are always good. But if your upgraded fleet was simply two caps, 28 enforcers, and 10 sentinels, then you brought a spoon to a knife fight. What I mentioned before should be about the same supply cost, and the strikecraft can go harass the sb while your ships stay out of range. So, if that fleet was the best you could put together, then I think what I listed would have been a better use of the supply for taking out a starbase.
back on topic, ves- Sins does a very good job of not letting any one unit rule all. So, yes, heavy cruisers and cap ships kick ass and can do tremendous amount of damage, but they are slow and very vulnerable to faster ships in quantity. One of the things I love about this game is every time you ask yourself 'which is better' you always have to ask yourself, "what am I trying to do." Ok, in the late game, what are you trying to do?