Not saying you're wrong, but why do you think that? I'd have thought the same thing about DNA, but I keep being told most DNA is junk (although I wouldn't be surprised to find out later we just don't know what it's for).
(a) Access for all but the smallest molecules to cells is tightly regulated by e.g. membrane transport proteins.
(b) similar to a, tissue where exchange with the outside world can occur, such as the intestine and lungs, are even more regulated and heavily guarded by the immune system. Apart from small molecules with the right lipofilicity, some minerals, potentially small peptides, or entities with other mechanisms of entry like viruses, nothing gets in (excluding endocytosis by e.g. immune cells).
(c) Anything entering the circulation will be processed by the liver eventually, where all kinds of enzymes target a broad range of structural motifs to break down molecules into 'non-foreign' building blocks to be reused.
(d) I can't think of any molecules not belonging to a particular known class. There is water, elemental ions, carbohydrates/sugars, peptides/proteins, lipids, and RNA/DNA, and small molecules (e.g. intermediate products). All of these except a subset of small molecules and heavy metals can be either broken down into 'known' parts or disposed of (not completely though; over time waste builds up which is likely part of why we age). Now if there are many inert small molecules, they would show up in all kinds of analytical tests. Inert or not, we can classify all of them chemically. There is a lot of stuff for which we don't know the exact function of course, and as these systems are highly complex and dynamic, functionality can be broad and context dependent.
By the way, the term junk DNA has various meanings in different contexts. In the context of non-codig DNA, this "junk" e.g. plays a role in epigenetic regulation as it influences physical accessibility for transcription. Also, DNA is relatively stable and unlikely to interfere with other cellular processes in the same way that random small molecules would.
I could definitely be wrong though. I'm almost done with my biomedical engineering masters, but over the years I turned to software and all the chem and bio knowledge is becoming rusty very quickly. It's also a field in which knowledge doesn't age well as it has been growing quite fast.
