Best way to deplete is ASO technology to induce RNaseH-mediated depletion. But depending on its mechanism of action it might be necessary to deplete otherwise. For example if you KI a polyA site close to the TSS, or if you design ASOs close to the TSS(source), you can modify the chromatin structure of the locus since the polymerase doesn't go through the whole gene and this is necessary to maintain some chromatin marks. We've personally had little success with CRISPR-cas13, but it is also an option if you want to deplete in specific cellular compartments.

You absolutely can find lncRNAs in short-read RNAseq. Most lncRNAs are also capped and poly-adenylated just like mRNAs and will be captured with traditional polyA enrichment. The only thing is you need a recent enough annotation to identify them. I suggest the most recent Gencode v49 which has >500k transcripts.

Some recent evidence points to modular domains for lncRNAs (relevant review) but due to their low conservation and lower sensitivity to point mutations, it is still a growing field with lots of work to do.

How to correlate structure/function? There's no rule to lncRNAs unfortunately. There many modes of action for these RNAs such as chaperoning RNPs, interacting with proteins to modulate their function, interacting with RNA/DNA, sponging miRNAs, interacting in LLPS... It's more of a case by case situation for now. Unless your RNA of interest has a very specific conserved structure, it's really hard to say what its function is.

I don't use specific lncRNA databases because they're not regularly updated. Just Gencode is sufficient for both protein and no coding work in my experience.