....are hitting statistics still subjective if comparing with individual players on the same team since they faced the same pitcher?
You will rarely have enough data against a given pitcher, at any level, to compare two hitters just on that data.
If you have enough games vs common opponents, you will eventually get enough data to compare players reasonably well, as the differences in opposition talent will even out over a large sample if the players are used similarly. This would be the case, for instance, at the pro level where guys are playing 100+ games vs a dozen or so teams a season.
At the HS level or college level, it's going to be much harder to make completely objective comparisons that are statistically valid, because the sample sizes won't be there.