Speedster Hose (noob question)

[Stevenarita]

Took my recently purchased 95 speedster and took on water as 2 (per engine hoses) quarter-inch, clear hoses broke -- one goes to the head (not sure where the other end goes) and a shorter hose that goes between the purple exhaust header to the muffler(?)

Was wondering why a thinner walled clear hose was used (assuming that I should be viewing something), and was thinking of using a thicker walled rubber line. Is this OK?

Thanks in advance for any help!