While I know some people have a very serious problem with this, my system (which is an Ivy Bridge based system - so it's not exactly new) barely has an issue with this at all. When a cap ship arrives, yes I can notice a barely perceptible hesitation - but for me, it really doesn't break game play (do I wish it wouldn't do it at all, sure. But it's not a deal-breaker for me).
There have been many theories in many threads as to why this happens - but nothing concrete/definitive. Most postulate that this occurs because the textures for an entire ship are loaded at the time of its appearance (and some have a LOT of textures). This could be the case I suppose. But is it indeed true?
There used to be a optional setting with earlier versions of the FSOpen (pre-3.8?) that allowed you to "preload all bitmaps at mission start" or something like that. Wouldn't that "cure" this issue, since all possible textures for any ships in a mission would already be loaded in video/RAM memory before they ever appear on screen (and thus be instantly available when the ship does arrive)? Or does FSOpen do this by default now, which is why the setting is now deprecated? But then, if FSOpen already preloads all mission textures/bitmaps before mission start by default, then this is likely NOT the cause of the hesitation issue and one must look elsewhere.