Reduce number of transcripts in a highly variable de novo transcriptome assembly
As you've suggested, CD-HIT works for reducing transcript numbers. We used a mixture of expression-based filtering and CD-HIT for reducing transcript counts for our genome-guided transcriptome assembly. This reduced numbers by a lot, without much change in BUSCO scores:


Map RNA-seq reads to Trinity-generated transcripts using Salmon
Use the expression of BUSCO genes to set a credible signal cutoff
Subset transcripts based on this threshold [for us it was 50 counts]
Identify the longest Met to Stop open reading frame for each transcript (may not be a good idea in all cases)
Run cdhit to collapse similar transcripts


Here's our CD-HIT command line:

cdhit -T 10 -c 0.98 -i longest_MetStopORF_HC50_TBNOCFED.fasta -o cdhit_0.98_LMOHC50_TBNOCFED.prot.fasta


More details here:

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0473-4#Sec9