My apologies if this is a duplicate request, but a quick search of the first few pages didn't find a similar thread to post in, hence this new one - please merge if I didn't look far enough back!
Anyway, my suggestion would be to enhance the display on the replication screen, so that you can confirm the name of items that only have a single copy in your inventory. For items with multiple copies in your inventory, an intermediate window pops up for you to select how many of that item to use as replicator fuel, at which time you can click the image of the item to confirm what it is. However, items with a single copy go directly into the replicator fuel window without the chance to double-check what exactly the item is (and if you click on the picture within the replicator fuel window, the item is simply returned to your full inventory list).
This is an issue when there are many items that use the same image, especially when you near your inventory's 1,000 unique item capacity.
Another additional feature that could act as a solution to this issue is a search function. As long as you know the useless equipment that you want to use as replicator fuel, a quick search that acts as a filter would help ensure the correct items are selected.
NOTE - an alternate solution, given the influx of new characters and their unique pieces of equipment, would be to simply increase or remove the inventory capacity of 1,000 unique items.
It's insane that there isn't any way to tell exactly what you're putting in the replicator as far as single-count items. I've been using the Crew Management Tool to help identify unneeded items and then dump those into the replicator, but as you say, it's impossible to do with certain items because so many things in the inventory have identical icons.
Last week, I had cleared out enough to bring my total unique item count down to 940 or something, and then this week it was back to 970. So I just went through and dumped a bunch of single items that were 3* or less, and which looked like they might belong only to a specific crew (clothing items, mainly). I figured even if I got rid of something that I needed, it wouldn't cost a lot to replicate a replacement for rare, uncommon, common, and basic items.
But we shouldn't need to do this.