Sure they weren't anachronistic, no one was saying that. The Connie III out of universe was a modified Shangri-La class, and thereby much more in-keeping with the aesthetic of a Kirk era starship. No one is arguing the ship isn't anachronistic, it had a retro look on-purpose in an effort to provide fan service and memberberries, that much we have already discussed to death on this forum. The Sagan nacelles imo are generic and dont match the look of any of the ships they are attached to. There was a vague intent to make them look maybe similar to the TMP Enterprise nacelles, but with the typical red bussards. I don't see any issue in Starfleet making ships that look retro or simply as a tribute to venerable starships of centuries past, especially in peace-time. As of 2401 there has been no mention of another major war since the Dominion Conflict and Starfleet has never been quoted as being a strictly military element of the Federation. So most of the time technology will advance and ships will become faster and more efficient, but there not a constant battle for tactical superiority in Starfleet as of 2401 simply because there is no need for it.
The nacelle design was made for the Stargazer to subtly imply an update from the Constitution class-style nacelles that Picard's Stargazer had. They weren't anachronistic in that sense because they were just meant to evoke the older design, not make it look 99% identical to it. Unfortunately, the rest of the Connie III was little more than the Shangri-La nonsensically upscaled with the barest of changes from the original ship. There was no on-screen stated reason why the ship looked the way it did, or why no other Starfleet ships were given that nostalgia aesthetic. Even the Excelsior II did not look like an old Excelsior with new nacelles. There were some behind-the-scenes rationale from Matalas, Blass and Drexler, but they seemed more like excuses rather than legitimately logical reasons. To me, there was no logical reason to make a brand-new ship from 2401 99% resemble a ship from the 2280's. Rios's Stargazer did not resemble Picard's Stargazer. So why did the Titan-A have to?