Most anything can be cut by a fair amount without compromising the quality, no matter how much we adore our lovely long sentences (and believe me, I absolutely adore mine). What is sacrificed in description may be gained in pace and/or focus, so it all comes out even. Which is why even short story editors don't obsess over a few hundred extra words in a submission, because if they like the story they will advise you on cutting it to fit to size and sharpen the prose at the same time.
None of which should be taken as advice to feel free to send in a 7,000 word story if they are asking for 5,000 or less. But there is no point in obsessing about whether you're using the right method to count the words. I've never seen submission guidelines that prescribe a specific method, but if there are magazines out there that do, then of course follow their instructions. But if they don't say, assume they'll be expecting an approximate word count from your word processor, and don't lose any sleep over it.