Recently I have started a new factorio run with goal to try out as many planet mods as it is possible. This mod seemed the best choice to have all them enabled in game. I put around 80 hours in this run and only then I noticed this warning

For anyone looking for a more playability focused planet modpack, please use Enable Planet Mods Lite, as it removes the most game-warping and least necessary planet mods, keeping the game more vanilla-focused until the space age era.

so now I'm wondering, will I have any troubles if I continue play with this mod? What difference will I feel other than that there are fewer planets?

If you've already put 80 hours into it, then you're way too far in for the changes to matter.

The biggest difference between the two packs is the removal of Lignumis and Muluna. Lignumis changes your starting planet from Nauvis, then gives you an early-tech, one-time-use method to get to Nauvis and begin the game proper (you can later revisit Lignumis during the interplanetary phase for new resources); Muluna changes your first required interplanetary destination, forcing you to make space science on the moon instead of a space platform.

The other missing planets (Janus, Terra Palus, Tenebris, and Naufulglebunusilo) had minimal planetary rewards, so their inclusion/exclusion shouldn't have much of an impact. Lignumis also has some other requirements that change many of the early-game recipes, which has repercussions all the way through to the interplanetary phase, to the point where growing wood is required in space for ammo (unless you disable it in the Lignumis settings)

If your 80 hours have already gotten you to space, then you might as well just stick with it. That statement you quoted isn't exactly a warning, just more of a notice, so that people know there is a better option (especially for those who don't want to deal with the monumental early-game changes of Lignumis and Muluna)

Thank you for the reply. I definitely want to have Lignumis and Muluna experience in this run.
Btw, Lignumis adds wood and steam science packs which is required in most researches from some point. This is why I'm planing expedition to back on Lignumis to set up production there.